X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 277.0
Details 200mM NH4Ac, 100mM (CH3)2AsO2Na, 25% PEG 8000, pH 6.0, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.68 α = 90
b = 65.68 β = 90
c = 139.89 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2007-03-04
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0000 PHOTON FACTORY BL-6A

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
2.7 59.46 99.4 0.052 -- -- 7.5 8967 n/a -- -- 68.7
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)
2.7 2.8 99.8 0.425 -- 4.9 6.5 --

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 2.7 59.46 -- 0.0 8967 8918 461 99.25 -- 0.2214 0.2201 0.2458 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 2.699 2.769 -- 27 609 0.241 0.467 -- 97.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 51.0192
RMS Deviations
Key Refinement Restraint Deviation
RIGID-BOND RESTRAINTS (A''2) 1.682
r_bond_refined_d 0.017
r_angle_refined_deg 1.435
r_dihedral_angle_1_deg 5.119
r_dihedral_angle_2_deg 38.569
r_dihedral_angle_3_deg 15.95
r_dihedral_angle_4_deg 18.64
CHIRAL-CENTER RESTRAINTS (A''3) 0.093
r_gen_planes_refined 0.006
MAIN-CHAIN BOND REFINED ATOMS (A''2) 1.23
MAIN-CHAIN ANGLE REFINED ATOMS (A''2) 2.193
SIDE-CHAIN BOND REFINED ATOMS (A''2) 2.995
SIDE-CHAIN ANGLE REFINED ATOMS (A''2) 4.594
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2008
Nucleic Acid Atoms 0
Heterogen Atoms 31
Solvent Atoms 79

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