X-dVal: X-ray Data Validation

phenix.xtriage / Matthew's Coefficient / Twinning Detection / CRYST Record analysis

This server uses software developed by the Phenix project, specifically the phenix.xtriage program, and software developed in our lab.

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Job 53 (Mar 25th, 2013 [02:09 PM])   → twinning detected

Your X-dVal Results

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Section
Summary
Completeness Plot
CRYST1 Record Search
Twin Detection Plot
Anisotropicity analyses
Twinning Analyses
Patterson analyses
Systematic absences
Wilson ratio and moments
L test for acentric data
Twinning and intensity statistics summary

Anisotropicity analyses

Anisotropicity ( [MaxAnisoB-MinAnisoB]/[MaxAnisoB] ) : 2.841e-16 Anisotropic ratio p-value : 0.000e+00 The p-value is a measure of of the severity of anisotropy as observed in the PDB. The p-value of 0.000e+00 indicates that roughly 100.0 % of dataset available in the PDB have an anisotropy equal or worse as compared to this dataset. For the resolution shell spanning between 3.08 - 2.99 Angstrom, the mean I/sigI is equal to 6.20. 55.1 % of these intensities have an I/sigI > 3. When sorting these intensities by their anisotropic correction factor and analysing the I/sigI behavior for this ordered list, we can gauge the presence of 'anisotropy induced noise amplification' in reciprocal space. The quarter of Intensities *least* affected by the anisotropy correction show : 6.87e+00 Fraction of I/sigI > 3 : 6.00e-01 ( Z = 2.20 ) The quarter of Intensities *most* affected by the anisotropy correction show : 4.20e+00 Fraction of I/sigI > 3 : 4.04e-01 ( Z = 6.61 ) The combined Z-score of 6.97 indicates that there probably is no significant systematic noise amplification. Z-scores are computed on the basis of a Bernoulli model assuming independence of weak reflections wrst anisotropy. Correcting for anisotropy in the data Some basic intensity statistics follow.

Low resolution completeness analyses

The following table shows the completeness of the data to 5 Angstrom. unused: - 86.7772 [ 0/2 ] 0.000 bin 1: 86.7772 - 10.7741 [549/556] 0.987 bin 2: 10.7741 - 8.5541 [521/522] 0.998 bin 3: 8.5541 - 7.4735 [509/510] 0.998 bin 4: 7.4735 - 6.7905 [505/507] 0.996 bin 5: 6.7905 - 6.3040 [490/501] 0.978 bin 6: 6.3040 - 5.9324 [497/506] 0.982 bin 7: 5.9324 - 5.6353 [495/504] 0.982 bin 8: 5.6353 - 5.3901 [491/501] 0.980 bin 9: 5.3901 - 5.1826 [463/476] 0.973 bin 10: 5.1826 - 5.0038 [514/526] 0.977 unused: 5.0038 - [ 0/0 ]

Mean intensity analyses

Analyses of the mean intensity. Inspired by: Morris et al. (2004). J. Synch. Rad.11, 56-59. The following resolution shells are worrisome: ------------------------------------------------ | d_spacing | z_score | compl. | / | ------------------------------------------------ None ------------------------------------------------

Possible outliers

Inspired by: Read, Acta Cryst. (1999). D55, 1759-1764 Acentric reflections: None

Centric reflections:

----------------------------------------------------------------- | d_space | H K L | |E| | p(wilson) | p(extreme) | ----------------------------------------------------------------- | 5.692 | 0, 24, 11 | 4.10 | 4.10e-05 | 7.03e-02 | ----------------------------------------------------------------- p(wilson) : 1-(erf[|E|/sqrt(2)]) p(extreme) : 1-(erf[|E|/sqrt(2)])^(n_acentrics) p(wilson) is the probability that an E-value of the specified value would be observed when it would selected at random from the given data set. p(extreme) is the probability that the largest |E| value is larger or equal than the observed largest |E| value. Both measures can be used for outlier detection. p(extreme) takes into account the size of the dataset.

Ice ring related problems

The following statistics were obtained from ice-ring insensitive resolution ranges mean bin z_score : 1.48 ( rms deviation : 1.03 ) mean bin completeness : 0.93 ( rms deviation : 0.21 ) The following table shows the z-scores and completeness in ice-ring sensitive areas. Large z-scores and high completeness in these resolution ranges might be a reason to re-assess your data processsing if ice rings were present. ------------------------------------------------ | d_spacing | z_score | compl. | Rel. Ice int. | ------------------------------------------------ | 3.897 | 2.42 | 0.97 | 1.000 | | 3.669 | 0.34 | 0.97 | 0.750 | | 3.441 | 2.32 | 0.97 | 0.530 | ------------------------------------------------ Abnormalities in mean intensity or completeness at resolution ranges with a relative ice ring intensity lower than 0.10 will be ignored. No ice ring related problems detected. If ice rings were present, the data does not look worse at ice ring related d_spacings as compared to the rest of the data set. Basic analyses completed ##----------------------------------------------------##