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 36% PEG300, 0.1 M MES (pH 6.5), 0.1 M NaCl

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 58.7 α = 90
b = 84.96 β = 90
c = 146.23 γ = 90
Symmetry
Space Group P 2 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 225 mm CCD -- 2013-04-20
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0 SPring-8 BL32XU

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
3.15 45.86 91.2 0.385 -- -- 10.167 -- 12096 -- -3.0 57.331
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)
3.15 3.23 99.5 1.369 -- 1.41 10.592 --

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 3.15 45.86 -- 0.0 -- 11508 564 91.23 -- 0.2673 0.2658 0.2998 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 3.15 3.231 -- 47 906 0.378 0.357 0.0 99.37
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 66.266
Anisotropic B[1][1] -0.29
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.75
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.47
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 12.841
r_dihedral_angle_1_deg 4.783
r_dihedral_angle_3_deg 18.957
r_gen_planes_refined 0.004
r_bond_refined_d 0.007
r_dihedral_angle_2_deg 38.109
r_chiral_restr 0.046
r_angle_refined_deg 1.043
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4167
Nucleic Acid Atoms 0
Heterogen Atoms 76
Solvent Atoms 56

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0158
XSCALE data scaling
PDB_EXTRACT data extraction version: 3.22
XDS data reduction
PHASER phasing
PHENIX refinement