X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 10% PEG3350, 20% glycerol, 0.12 M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.5 α = 90
b = 113.07 β = 96.96
c = 73.22 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2011-08-16
Diffraction Radiation
Monochromator Protocol
cryo-cooled double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.97949 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
2.35 113.07 99.6 0.041 0.041 -- 3.8 46629 46629 0.0 0.0 65.21
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)
2.35 2.48 99.9 0.678 0.678 1.1 3.8 6803

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 2.35 72.68 0.0 0.0 46593 46593 2347 99.53 0.208 0.208 0.2069 0.2288 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 2.35 2.41 3438 181 3257 0.237 0.2643 -- 99.53
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 69.3759
Anisotropic B[1][1] -0.9496
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 6.4574
Anisotropic B[2][2] -10.97
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 11.9196
RMS Deviations
Key Refinement Restraint Deviation
t_gen_planes 0.015
t_it 1.289
t_omega_torsion 2.85
t_angle_deg 1.15
t_trig_c_planes 0.0068
t_torsion_other 17.39
t_dihedral_angle_d 17.39
t_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.331
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6485
Nucleic Acid Atoms 0
Heterogen Atoms 99
Solvent Atoms 247

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.16
BUSTER-TNT refinement
PDB_EXTRACT data extraction version: 3.11
XDS data scaling
XDS data reduction
PHASER phasing
BUSTER refinement