X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

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_angle_refined_deg 1.732
r_gen_planes_refined 0.008
r_dihedral_angle_1_deg 7.708
r_dihedral_angle_4_deg 22.029
r_dihedral_angle_3_deg 20.927
r_dihedral_angle_2_deg 37.352
r_bond_refined_d 0.014
r_chiral_restr 0.124
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

Software
Software Name Purpose
SCALA data scaling version: 3.3.16
REFMAC refinement version: 5.6.0117
PDB_EXTRACT data extraction version: 3.11
Blu-Ice data collection
XSCALE data scaling
MOLREP phasing version: (CCP4 6.2)