X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 277.0
Details 100 mM Sodium Sulphate, 2.4 M Sodium Malonate, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.45 α = 90
b = 65.45 β = 90
c = 72.29 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 2M -- 2012-09-15
Diffraction Radiation
Monochromator Protocol
Si(111) double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1

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
1.97 56.68 99.6 0.437 -- -- 10.4 130244 12508 -- -- --
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)
1.97 2.02 100.0 0.026 -- 1.1 10.7 886

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 2.0 29.81 -- 0.0 -- 11894 569 99.48 -- 0.1874 0.1844 0.2452 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 2.0 2.052 -- 37 841 0.324 0.475 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.8705
Anisotropic B[1][1] 0.01
Anisotropic B[1][2] 0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.04
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 15.756
r_gen_planes_other 0.005
r_dihedral_angle_2_deg 36.367
r_bond_refined_d 0.019
r_chiral_restr 0.101
r_dihedral_angle_1_deg 5.845
r_bond_other_d 0.006
r_gen_planes_refined 0.009
r_angle_refined_deg 1.875
r_dihedral_angle_3_deg 18.018
r_angle_other_deg 1.321
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1212
Nucleic Acid Atoms 0
Heterogen Atoms 7
Solvent Atoms 87

Software

Software
Software Name Purpose
MOSFLM data reduction
Aimless data scaling version: 0.1.26
PHASER phasing version: 2.5.1
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
GDA data collection