X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 287.0
Details 12% PEG 3350, 0.1M sodium malonate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.13 α = 90
b = 116.13 β = 90
c = 119.18 γ = 90
Symmetry
Space Group I 41 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 2011-06-11
Diffraction Radiation
Monochromator Protocol
Ni FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 0.9792 -- --

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
2.49 50 99.7 -- -- -- -- 14624 14571 -- -- --
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)
2.49 2.53 100.0 0.459 0.407 7.71 10.8 715

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 2.49 50.0 -- -- -- 13829 731 99.62 -- 0.2167 0.21392 0.27358 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 2.49 2.553 -- 66 972 0.284 0.355 -- 99.62
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.177
Anisotropic B[1][1] -1.54
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.54
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.08
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.302
r_scbond_it 1.349
r_mcangle_it 1.094
r_mcbond_it 0.588
r_gen_planes_refined 0.005
r_chiral_restr 0.08
r_dihedral_angle_4_deg 15.386
r_dihedral_angle_3_deg 15.665
r_dihedral_angle_2_deg 37.424
r_dihedral_angle_1_deg 6.003
r_angle_refined_deg 1.182
r_bond_refined_d 0.01
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2501
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 20

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
Molrep Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0109 refinement
Molrep model building
HKL-2000 data collection