X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 291.0
Details 0.5M (NH4)2SO4, 100mM tri-sodium citrate, 0.8M Li2SO4, pH 5.6, vapor diffusion, hanging drop, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.1 α = 90
b = 83.1 β = 90
c = 153 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2008-03-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BSRF BEAMLINE 1W2B 1.0000 BSRF 1W2B

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
2.4 76.51 99.9 0.063 -- -- 4.7 23421 n/a -- -- 52.2
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)
2.4 2.49 100.0 -- -- -- -- --

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 2.4 76.51 -- 0.0 23421 23395 1188 99.74 -- 0.2107 0.2087 0.2492 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 2.398 2.46 -- 55 1639 0.234 0.211 -- 97.86
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.8183
RMS Deviations
Key Refinement Restraint Deviation
RIGID-BOND RESTRAINTS (A''2) 1.627
r_bond_refined_d 0.006
r_angle_refined_deg 1.137
r_dihedral_angle_1_deg 4.364
r_dihedral_angle_2_deg 38.163
r_dihedral_angle_3_deg 16.343
r_dihedral_angle_4_deg 12.968
CHIRAL-CENTER RESTRAINTS (A''3) 0.119
r_gen_planes_refined 0.003
MAIN-CHAIN BOND REFINED ATOMS (A''2) 1.591
MAIN-CHAIN ANGLE REFINED ATOMS (A''2) 2.928
SIDE-CHAIN BOND REFINED ATOMS (A''2) 2.343
SIDE-CHAIN ANGLE REFINED ATOMS (A''2) 4.203
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4420
Nucleic Acid Atoms 0
Heterogen Atoms 62
Solvent Atoms 136

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
CNS Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.5.0109 refinement