X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 20% PEG 3350, 0.15M DL-Malic acid

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 98.2 α = 90
b = 133 β = 112
c = 101.5 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 315r -- 2012-10-29
Diffraction Radiation
Monochromator Protocol
Numerical link type Si(111) double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A

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
2.3 94.11 99.7 0.081 -- -- 3.785 -- 106954 -- -3.0 41.091
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)
2.3 2.42 99.8 0.472 -- 3.24 3.805 --

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 2.3 94.11 -- 0.0 -- 104920 2009 99.78 -- 0.2208 0.2198 0.2729 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 2.3 2.36 -- 142 7756 0.318 0.36 0.0 99.82
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.168
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.01
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.01
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.399
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
r_angle_refined_deg 1.726
r_chiral_restr 0.094
r_angle_other_deg 0.872
r_bond_refined_d 0.015
r_dihedral_angle_2_deg 34.921
r_dihedral_angle_3_deg 16.85
r_dihedral_angle_4_deg 21.067
r_bond_other_d 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 17220
Nucleic Acid Atoms 0
Heterogen Atoms 212
Solvent Atoms 309

Software

Software
Software Name Purpose
XDS data processing
XSCALE data scaling
MOLREP phasing
REFMAC refinement version: 5.8.0073
PDB_EXTRACT data extraction version: 3.22