X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 293.0
Details salt, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 204.74 α = 90
b = 204.74 β = 90
c = 152.95 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm dynamically bendable mirror 2007-12-03
Diffraction Radiation
Monochromator Protocol
LN2 cooled fixed-exit Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 0.9999 SLS X06SA

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
3.1 47.25 95.1 0.14 -- -- 3.8 28238 28238 0.0 0.0 --
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)
3.1 3.17 85.9 0.795 -- -- 3.0 --

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 3.1 47.25 0.0 0.0 26825 26825 1412 100.0 0.22413 0.22413 0.22166 0.27158 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 3.1 3.182 -- 96 1816 0.359 0.344 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 68.488
Anisotropic B[1][1] -1.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.52
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.04
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.016
r_scbond_it 1.297
r_mcangle_it 1.326
r_mcbond_other 0.101
r_mcbond_it 1.16
r_symmetry_hbond_refined 0.102
r_symmetry_vdw_other 0.205
r_symmetry_vdw_refined 0.218
r_xyhbond_nbd_refined 0.144
r_nbtor_other 0.087
r_nbtor_refined 0.184
r_nbd_other 0.187
r_bond_refined_d 0.01
r_bond_other_d 0.001
r_angle_refined_deg 1.266
r_angle_other_deg 0.789
r_dihedral_angle_1_deg 7.012
r_dihedral_angle_2_deg 37.695
r_dihedral_angle_3_deg 18.487
r_dihedral_angle_4_deg 17.688
r_chiral_restr 0.067
r_gen_planes_refined 0.003
r_gen_planes_other 0.002
r_nbd_refined 0.219
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6367
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 15

Software

Computing
Computing Package Purpose
OTHER Data Collection
XDS Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.2.0005 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.2.0005 refinement
MOLREP model building
OTHER data collection