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 = 42.01 α = 90
b = 41.34 β = 104.14
c = 72.19 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
1.15 70.01 91.4 -- 0.063 -- 7.0 -- 77998 0.0 0.0 10.186
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)
1.15 1.21 72.0 0.189 0.189 4.0 6.7 8923

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 1.15 40.74 -- 0.0 77978 77978 7910 91.01 0.14 0.14 0.137 0.168 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 1.149 1.179 -- 384 3207 0.162 0.199 -- 56.65
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.922
Anisotropic B[1][1] 0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.12
Anisotropic B[2][2] -0.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.01
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.024
r_gen_planes_refined 0.014
r_angle_refined_deg 2.448
r_sphericity_free 22.712
r_chiral_restr 0.168
r_rigid_bond_restr 8.976
r_sphericity_bonded 14.336
r_dihedral_angle_1_deg 7.018
r_dihedral_angle_4_deg 20.563
r_dihedral_angle_2_deg 36.144
r_dihedral_angle_3_deg 14.055
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2055
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 292

Software

Software
Software Name Purpose
REFMAC refinement
SCALA data scaling version: 3.3.20
PDB_EXTRACT data extraction version: 3.006