X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6
Temperature 298.0
Details 0.1M PIPES, 17% PEG3350, 18% Glycerol

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 156.5 α = 90
b = 136.86 β = 90.41
c = 107.84 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r -- 2013-03-15
Diffraction Radiation
Monochromator Protocol
double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U

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
2.8 50 99.7 0.09 -- 13.992 4.2 -- 56472 -- -- --
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)
2.8 2.9 99.9 0.763 -- -- 4.1 5644

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 2.8 50.0 -- 0.0 -- 50792 2627 95.43 -- 0.1998 0.1983 0.2307 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 2.8 2.873 -- 105 2331 0.278 0.336 -- 59.4
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 53.457
Anisotropic B[1][1] 0.36
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.06
Anisotropic B[2][2] 0.21
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.56
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_mcbond_it 3.107
r_bond_other_d 0.002
r_dihedral_angle_2_deg 35.493
r_mcangle_it 5.034
r_mcbond_other 3.101
r_dihedral_angle_4_deg 18.736
r_chiral_restr 0.077
r_angle_other_deg 0.867
r_bond_refined_d 0.01
r_gen_planes_other 0.002
r_angle_refined_deg 1.391
r_dihedral_angle_1_deg 6.615
r_dihedral_angle_3_deg 17.209
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10214
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 139

Software

Software
Software Name Purpose
HKL-2000 data reduction
REFMAC refinement version: 5.8.0073
PDB_EXTRACT data extraction version: 3.15
HKL-2000 data scaling
PHASER phasing