X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 292.0
Details 1.0-1.2 M sodium malonate pH 7.0-8.0

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 228.92 α = 90
b = 228.92 β = 90
c = 78.92 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 6M -- 2015-04-04
Diffraction Radiation
Monochromator Protocol
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9792 APS 24-ID-C

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.9 50 99.9 -- 0.1 -- 13.5 -- 164734 -- -- 26.35
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.9 1.93 99.6 0.776 -- 4.06 11.9 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.9 49.471 -- 1.34 -- 163752 4917 99.82 -- 0.2153 0.2144 0.2444 random
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.9216 1.9442 -- 410 4924 0.3003 0.3233 -- 100.0
X Ray Diffraction 1.9679 1.9928 -- 410 4969 0.2866 0.3135 -- 100.0
X Ray Diffraction 2.0467 2.076 -- 409 4994 0.2734 0.2971 -- 100.0
X Ray Diffraction 2.1069 2.1399 -- 410 5032 0.2619 0.2825 -- 100.0
X Ray Diffraction 2.2125 2.2527 -- 410 5040 0.2552 0.2879 -- 100.0
X Ray Diffraction 2.296 2.3429 -- 410 5022 0.248 0.2858 -- 100.0
X Ray Diffraction 2.4495 2.5108 -- 408 5028 0.2383 0.2553 -- 100.0
X Ray Diffraction 2.5786 2.6545 -- 410 5038 0.2443 0.2773 -- 100.0
X Ray Diffraction 2.8381 2.9517 -- 410 5062 0.2254 0.2659 -- 100.0
X Ray Diffraction 3.0861 3.2487 -- 410 5049 0.218 0.2374 -- 100.0
X Ray Diffraction 3.7187 4.0928 -- 410 5136 0.1737 0.1985 -- 100.0
X Ray Diffraction 4.6846 5.9006 -- 410 5188 0.1514 0.1857 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.1
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.039
f_dihedral_angle_d 16.321
f_plane_restr 0.004
f_bond_d 0.003
f_angle_d 0.616
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12666
Nucleic Acid Atoms 0
Heterogen Atoms 44
Solvent Atoms 1588

Software

Software
Software Name Purpose
PHENIX refinement version: (1.10_2155: ???)
HKL-2000 data reduction
HKL-2000 data scaling
PHASER phasing