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 = 42.12 α = 90
b = 41.19 β = 104.19
c = 71.81 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 -- 2014-01-01
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
1.12 41.19 95.8 0.076 0.076 -- 6.5 -- 87368 0.0 0.0 9.25
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)
1.12 1.18 80.2 0.166 0.166 3.8 5.1 10618

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 1.12 39.73 -- 0.0 87346 87346 8792 95.77 0.131 0.131 0.128 0.154 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 1.123 1.152 -- 434 4056 0.126 0.16 -- 66.42
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.965
Anisotropic B[1][1] 0.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.01
Anisotropic B[2][2] -0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.09
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 11.196
r_dihedral_angle_2_deg 32.502
r_dihedral_angle_4_deg 19.99
r_angle_refined_deg 2.605
r_dihedral_angle_1_deg 6.761
r_chiral_restr 0.154
r_gen_planes_refined 0.016
r_bond_refined_d 0.025
r_rigid_bond_restr 10.008
r_dihedral_angle_3_deg 12.641
r_sphericity_free 23.139
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2049
Nucleic Acid Atoms 0
Heterogen Atoms 35
Solvent Atoms 299

Software

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