X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details 0.20M sodium acetate, 30.00% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 57.82 α = 90
b = 57.82 β = 90
c = 63.89 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 KOHZU: Double Crystal Si(111) 2012-09-19
Diffraction Radiation
Monochromator Protocol
Double Crystal Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.2.2 0.979095,0.979338,0.953725 ALS 8.2.2

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
1.8 28.91 100.0 -- 0.103 -- 13.3 11856 11856 -- -- 26.12
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)
1.8 1.85 100.0 0.014 1.374 0.6 8.0 843

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
MAD 1.8 28.91 -- 0.0 -- 11834 562 99.97 -- 0.1966 0.1953 0.2228 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 1.8 1.847 -- 32 814 0.311 0.357 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 33.7023
Anisotropic B[1][1] 0.49
Anisotropic B[1][2] 0.49
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.61
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.001
r_gen_planes_refined 0.005
r_chiral_restr 0.078
r_dihedral_angle_4_deg 18.443
r_dihedral_angle_3_deg 13.99
r_dihedral_angle_2_deg 30.821
r_dihedral_angle_1_deg 5.462
r_angle_other_deg 0.732
r_angle_refined_deg 1.361
r_bond_other_d 0.001
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 751
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 72

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
REFMAC5 version: 5.7.0029 refinement
SCALA version: 3.3.20 phasing
SOLVE phasing
pdb_extract version: 3.10 data extraction
MOLPROBITY version: 3beta29 validation