X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.5
Temperature 298.0
Details 27% PEGMME 2K, 0.1 M Na acetate pH 4.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.16 α = 90
b = 68.84 β = 90
c = 104.26 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL PSI PILATUS 6M -- 2014-05-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID23-2 0.87260 ESRF ID23-2

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 57.45 100.0 0.078 -- 8.2 6.6 26612 26612 -- -- --
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)
2.0 2.05 100.0 0.601 -- 2.6 6.2 --

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
-- 2.0 57.45 -- -- -- 25217 1344 99.97 -- 0.18415 0.18114 0.2437 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 2.0 2.052 -- 96 1863 0.247 0.288 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 34.275
Anisotropic B[1][1] 0.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.23
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.95
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_other 3.769
r_long_range_B_refined 7.705
r_dihedral_angle_1_deg 6.634
r_bond_refined_d 0.018
r_mcangle_it 4.007
r_angle_refined_deg 1.819
r_chiral_restr 0.105
r_bond_other_d 0.001
r_gen_planes_refined 0.008
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 16.315
r_mcbond_other 2.816
r_mcangle_other 4.006
r_scangle_other 5.903
r_long_range_B_other 7.676
r_angle_other_deg 0.833
r_mcbond_it 2.817
r_scbond_it 3.769
r_dihedral_angle_2_deg 37.676
r_dihedral_angle_4_deg 20.506
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2974
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 187

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0049
XDS data reduction
Aimless data scaling
MOLREP phasing