X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
Temperature 277.0
Details 0.2M magnesium formate dehydrate, 15.0% w/v polyethylene glycol 3350, 20% v/v glycerol as cryoprotectant

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.79 α = 89.18
b = 55.1 β = 86.24
c = 127.76 γ = 78.2
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 95
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX-225 -- 2015-02-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1.0000 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
2.11 42.49 92.1 0.072 -- -- 2.0 -- 56154 -- -- --
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)
2.11 2.16 95.8 0.317 -- 1.8 2.0 --

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 2.11 25.0 -- 0.0 -- 53398 2724 92.04 -- 0.2478 0.2459 0.2853 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 2.11 2.164 -- 210 4034 0.357 0.376 -- 95.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 38.604
Anisotropic B[1][1] 1.72
Anisotropic B[1][2] 0.86
Anisotropic B[1][3] 1.39
Anisotropic B[2][2] -0.39
Anisotropic B[2][3] 1.52
Anisotropic B[3][3] -0.79
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.004
r_dihedral_angle_2_deg 37.229
r_chiral_restr 0.06
r_angle_refined_deg 1.062
r_mcbond_it 0.717
r_scbond_it 0.46
r_bond_refined_d 0.007
r_dihedral_angle_3_deg 13.38
r_dihedral_angle_4_deg 12.572
r_mcangle_it 1.332
r_dihedral_angle_1_deg 4.827
Coordinate Error
Parameter Value
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7895
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 322

Software

Software
Software Name Purpose
XDS data processing
Aimless data scaling
REFMAC refinement version: 5.8.0135
PDB_EXTRACT data extraction version: 3.20