X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 291.0
Details Crystallization buffer was 0.1M sodium BICINE, pH 9, 0.2 M ammonium sulfate and 2M sodium malonate pH 7 made from 1M sodium BICINE and 3.4M sodium malonate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 42.1 α = 90
b = 40.97 β = 104.14
c = 71.69 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
PIXEL PSI PILATUS 6M -- 2013-05-21
Diffraction Radiation
Monochromator Protocol
High Heat Load (HHL) Monochromator: Si 111; Large Offset Monochromator (LOM) : Si 311, Si 511 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.826606 PETRA III, EMBL c/o DESY P13 (MX1)

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
1.06 69.52 93.5 -- 0.051 -- 6.7 -- 100624 0.0 0.0 9.034
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)
1.06 1.12 77.6 0.376 0.376 2.0 6.0 12110

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
MR 1.06 40.82 -- 0.0 100617 100617 10084 93.38 0.138 0.138 0.135 0.162 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 1.059 1.087 -- 530 4620 0.194 0.22 -- 64.77
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.575
Anisotropic B[1][1] 0.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.03
Anisotropic B[2][2] -0.17
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.12
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.151
r_dihedral_angle_4_deg 22.584
r_gen_planes_refined 0.015
r_sphericity_bonded 11.072
r_bond_refined_d 0.026
r_rigid_bond_restr 9.29
r_angle_refined_deg 2.588
r_dihedral_angle_1_deg 7.091
r_dihedral_angle_2_deg 35.885
r_dihedral_angle_3_deg 14.009
r_sphericity_free 24.512
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2058
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 277

Software

Software
Software Name Purpose
REFMAC refinement
SCALA data scaling version: 3.3.20
PDB_EXTRACT data extraction version: 3.006
HKL-2000 data collection
XDS data reduction
MOLREP phasing