X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 7.1
Temperature 291.0
Details (NH4)2HPO4 0.6M, pH 7.1, vapor diffusion, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 129.26 α = 90
b = 129.26 β = 90
c = 129.26 γ = 90
Symmetry
Space Group I 2 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2011-03-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.979417 AUSTRALIAN SYNCHROTRON MX2

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
2.15 40.88 100.0 0.126 0.126 -- 21.7 19684 19684 0.0 0.0 23.6
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)
2.15 2.27 100.0 0.458 0.458 7.7 22.1 2848

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 2.15 40.876 -- 0.0 -- 19671 1006 99.91 -- 0.1692 0.167 0.2106 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 2.15 2.206 -- 79 1372 0.175 0.215 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 26.5934
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 4.05
r_scbond_it 2.5
r_mcangle_it 1.471
r_mcbond_other 0.207
r_bond_refined_d 0.016
r_bond_other_d 0.001
r_angle_refined_deg 1.491
r_angle_other_deg 0.961
r_dihedral_angle_1_deg 5.921
r_dihedral_angle_2_deg 30.147
r_dihedral_angle_3_deg 15.762
r_dihedral_angle_4_deg 20.005
r_chiral_restr 0.107
r_gen_planes_refined 0.006
r_gen_planes_other 0.001
r_mcbond_it 0.766
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.178
Luzzati ESD (R-Free Set) 0.161
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2064
Nucleic Acid Atoms 0
Heterogen Atoms 14
Solvent Atoms 182

Software

Computing
Computing Package Purpose
Blu-Ice Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
Phaser version: 2.1.4 molecular replacement
SCALA version: 3.3.16 data reduction
Mosflm data collection