X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 0.2 M Sodium-Malonate, 40% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.23 α = 90
b = 127.15 β = 90
c = 265.5 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 -- 2014-07-19
Diffraction Radiation
Monochromator Protocol
LN2 cooled fixed-exit. Si(111) monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06SA 1.0 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
2.8 30 96.2 0.096 -- -- 4.7 81904 78792 2.0 2.0 --
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)
2.8 2.9 98.1 0.48 -- 3.5 -- --

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 2.8 30.0 2.0 -- 78758 74817 3941 96.21 -- 0.18144 0.17962 0.21573 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 2.8 2.873 -- 292 5553 0.286 0.337 -- 98.22
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 47.426
Anisotropic B[1][1] -1.03
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.29
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.74
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.024
r_angle_refined_deg 0.919
r_dihedral_angle_4_deg 20.581
r_chiral_restr 0.066
r_sphericity_bonded 20.632
r_dihedral_angle_3_deg 18.353
r_long_range_B_refined 3.333
r_sphericity_free 31.771
r_bond_refined_d 0.004
r_gen_planes_refined 0.003
r_mcangle_it 2.473
r_mcbond_it 1.93
r_dihedral_angle_2_deg 36.954
r_rigid_bond_restr 0.796
r_scbond_it 2.53
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 19674
Nucleic Acid Atoms 0
Heterogen Atoms 63
Solvent Atoms 155

Software

Software
Software Name Purpose
XDS data scaling
PHASER phasing
REFMAC refinement version: 5.7.0032
XDS data reduction
XSCALE data scaling