X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 298.0
Details Protein at 30 mg/ml, 26% PEG 6000, 0.05M HEPES, 0.1M Magnesium chloride, 0.02M Potassium ADP, 0.25M Sodium nitrate, 0.025M Sodium azide, 0.005M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 65.39 α = 90
b = 70.31 β = 90
c = 80.32 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2002-09-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R 1.541 -- --

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
2.09 17.64 92.14 -- -- -- -- 20717 20717 1.0 1.0 --
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)
2.091 2.252 81.0 -- -- -- -- --

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
ISOMORPHOUS WITH PDB ENTRY 1M15 2.091 17.635 -- 1.0 20717 20717 636 92.14 -- 0.1761 0.175 0.2109 Used same test set as PDB entry 1M15
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 2.0906 2.2517 -- 115 3460 0.2192 0.2525 -- 81.0
X Ray Diffraction 2.2517 2.4777 -- 127 3895 0.2007 0.2523 -- 91.0
X Ray Diffraction 2.4777 2.835 -- 123 4064 0.1992 0.2594 -- 94.0
X Ray Diffraction 2.835 3.5669 -- 137 4218 0.1862 0.2289 -- 97.0
X Ray Diffraction 3.5669 17.6354 -- 134 4444 0.1469 0.1642 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Anisotropic B[1][1] -8.2654
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 15.1452
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.8797
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.006
f_chiral_restr 0.067
f_dihedral_angle_d 14.37
f_angle_d 0.975
f_bond_d 0.006
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2817
Nucleic Acid Atoms 0
Heterogen Atoms 40
Solvent Atoms 258

Software

Computing
Computing Package Purpose
CrystalClear Data Collection
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHENIX (phenix.refine: 1.7_650) Structure Solution
PHENIX (phenix.refine: 1.7_650) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.7_650) refinement
PHENIX version: (phenix.refine: 1.7_650) model building
CrystalClear data collection