X-RAY DIFFRACTION Experimental Data & Validation


Lost? View more X-Ray Crystallographic info.

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 300.0
Details 20% polyethylene glycol 3350, 0.4M sodium malonate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 115.38 α = 90
b = 115.38 β = 90
c = 282.54 γ = 120
Symmetry
Space Group P 31 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2012-04-05
Diffraction Radiation
Monochromator Protocol
Liquid nitrogen cooled double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL12-2 0.97950 SSRL BL12-2

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
3 37.43 99.6 -- 0.052 -- 4.9 43376 43376 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)
3.0 3.16 99.6 0.381 0.381 2.0 4.8 --

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 3.0 37.43 -- -- 43315 41124 2188 99.47 -- 0.24164 0.2389 0.29377 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 3.0 3.077 -- 165 2841 0.324 0.362 -- 99.21
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 130.915
Anisotropic B[1][1] 0.49
Anisotropic B[1][2] 0.25
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.74
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.008
r_chiral_restr 0.124
r_dihedral_angle_4_deg 22.029
r_dihedral_angle_3_deg 20.927
r_dihedral_angle_2_deg 37.352
r_dihedral_angle_1_deg 7.708
r_angle_refined_deg 1.732
r_bond_refined_d 0.014
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 9867
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 2

Software

Computing
Computing Package Purpose
Bluice Data Collection
XSCALE Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Molrep (CCP4 6.2) Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.6.0117 refinement
SCALA version: 3.3.16 data reduction