X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 295.0
Details 0.1M MES pH 6.5 1.8M ammonium sulphate 0.010M cobalt chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 66.25 α = 90
b = 66.25 β = 90
c = 118.01 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RIGAKU SATURN 944 -- 2011-07-14
CCD MAR CCD 165 mm -- 2011-07-29
Diffraction Radiation
Monochromator Protocol
VARIMAX HF SINGLE WAVELENGTH
Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4C 0.979 NSLS X4C
ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418 -- --

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
2.45 50 97.8 0.088 -- -- 5.3 11441 11190 0.0 -3.0 --
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)
2.45 2.49 88.2 0.402 -- -- 2.5 473

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
SAD 2.456 41.132 -- 0.0 11973 11183 537 97.88 0.1881 0.1881 0.1864 0.2198 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 2.4559 2.703 -- 115 2508 0.2616 0.3176 -- 95.0
X Ray Diffraction 2.703 3.094 -- 157 2650 0.2003 0.2533 -- 99.0
X Ray Diffraction 3.094 3.8976 -- 131 2697 0.1768 0.2164 -- 99.0
X Ray Diffraction 3.8976 41.1381 -- 134 2791 0.1701 0.1885 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.1491
Anisotropic B[1][1] 7.8379
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 7.8379
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -15.6759
RMS Deviations
Key Refinement Restraint Deviation
f_chiral_restr 0.081
f_dihedral_angle_d 13.847
f_bond_d 0.014
f_plane_restr 0.005
f_angle_d 1.364
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1258
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 77

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
SHARP phasing
SOLOMON phasing
PHENIX refinement version: 1.7_650
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling