X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 277.0
Details 0.1 M MMT buffer, 100 mM Sodium Sulphate, 25% PEG 1500, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 34.76 α = 110.47
b = 34.78 β = 105.6
c = 41.86 γ = 96
Symmetry
Space Group P 1

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
1.38 37.05 83.5 0.049 -- -- 3.8 112030 31070 -- -- --
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)
1.38 1.41 83.8 0.37 -- 4.0 3.8 1570

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 1.38 25.79 -- 0.0 -- 29524 1470 83.53 -- 0.1505 0.1489 0.1815 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 1.382 1.418 -- 98 2049 0.179 0.203 -- 83.06
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.78
Anisotropic B[1][1] 0.02
Anisotropic B[1][2] 0.04
Anisotropic B[1][3] 0.02
Anisotropic B[2][2] -0.02
Anisotropic B[2][3] -0.02
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.002
r_gen_planes_refined 0.014
r_chiral_restr 0.177
r_dihedral_angle_4_deg 22.762
r_dihedral_angle_3_deg 13.517
r_dihedral_angle_2_deg 20.565
r_dihedral_angle_1_deg 5.032
r_angle_other_deg 1.106
r_angle_refined_deg 2.696
r_bond_other_d 0.002
r_bond_refined_d 0.03
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1258
Nucleic Acid Atoms 0
Heterogen Atoms 45
Solvent Atoms 78

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