X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.5
Temperature 293.7
Details pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.7K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.89 α = 90
b = 114.85 β = 93.98
c = 66.82 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210 -- --
Diffraction Radiation
Monochromator Protocol
Si 111 CHANNEL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.000 SPring-8 BL38B1

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
1.9 50 99.8 0.089 0.089 -- 2.5 51972 51972 0.0 0.0 --
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)
1.9 1.97 99.4 0.611 0.611 1.9 2.4 5175

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 1.9 28.83 -- -- -- 49319 2653 99.68 -- 0.18263 0.1806 0.22056 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 1.897 1.947 -- 181 3552 0.288 0.311 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.665
Anisotropic B[1][1] -0.06
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.03
Anisotropic B[2][2] 0.03
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.03
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.004
r_mcangle_it 0.529
r_angle_refined_deg 0.965
r_bond_refined_d 0.007
r_mcbond_it 0.286
r_dihedral_angle_1_deg 5.129
r_scbond_it 0.843
r_dihedral_angle_2_deg 34.197
r_scangle_it 1.34
r_chiral_restr 0.071
r_dihedral_angle_4_deg 16.335
r_dihedral_angle_3_deg 13.417
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5502
Nucleic Acid Atoms 0
Heterogen Atoms 46
Solvent Atoms 561

Software

Software
Software Name Purpose
PHASER phasing
REFMAC refinement version: 5.5.0102
HKL-2000 data reduction
HKL-2000 data scaling