XdVal: Xray 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.
Job 53 (Mar 25th, 2013 [02:09 PM]) → twinning detected
Your XdVal Results
Back to front page
 Anisotropicity analyses
Anisotropicity ( [MaxAnisoBMinAnisoB]/[MaxAnisoB] ) : 2.841e16
Anisotropic ratio pvalue : 0.000e+00
The pvalue is a measure of of the severity of anisotropy as observed in the PDB.
The pvalue 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 : 6.00e01 ( Z = 2.20 )
The quarter of Intensities *most* affected by the anisotropy correction show
: 4.20e+00
Fraction of I/sigI > 3 : 4.04e01 ( Z = 6.61 )
The combined Zscore of 6.97 indicates that there probably is no significant systematic
noise amplification.
Zscores 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, 5659.
The following resolution shells are worrisome:

 d_spacing  z_score  compl.  / 

None

Possible outliers
Inspired by: Read, Acta Cryst. (1999). D55, 17591764
Acentric reflections:
None
Centric reflections:

 d_space  H K L  E  p(wilson)  p(extreme) 

 5.692  0, 24, 11  4.10  4.10e05  7.03e02 

p(wilson) : 1(erf[E/sqrt(2)])
p(extreme) : 1(erf[E/sqrt(2)])^(n_acentrics)
p(wilson) is the probability that an Evalue 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 icering
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 zscores
and completeness in icering sensitive areas.
Large zscores and high completeness in these
resolution ranges might be a reason to reassess
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
####
