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
AREA DETECTOR 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_gen_planes_other 0.005
r_gen_planes_refined 0.009
r_chiral_restr 0.101
r_dihedral_angle_4_deg 15.756
r_dihedral_angle_3_deg 18.018
r_dihedral_angle_2_deg 36.367
r_dihedral_angle_1_deg 5.845
r_angle_other_deg 1.321
r_angle_refined_deg 1.875
r_bond_other_d 0.006
r_bond_refined_d 0.019
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

Computing
Computing Package Purpose
GDA Data Collection
MOSFLM Data Reduction (intensity integration)
Aimless Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 refinement
Phaser version: 2.5.1 molecular replacement
AIMLESS version: 0.1.26 data reduction
Mosflm data collection