X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details 2 M dihydrogen phosphate, MES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 69.64 α = 90
b = 69.64 β = 90
c = 92.85 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 collimating mirror 2002-06-01
Diffraction Radiation
Monochromator Protocol
mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X8C 1.100 NSLS X8C

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
1.8 50 98.2 -- 0.08 -- 7.8 25953 25953 0.0 0.0 17.3
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)
1.8 1.86 96.7 -- 0.454 4.6 -- --

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
two wavelength anomalous dispersion 1.8 50.58 -- 0.0 23890 23890 2419 96.8 0.184 0.182 0.182 0.202 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 1.8 1.91 -- 387 3368 0.201 0.239 0.012 93.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 23.9
Anisotropic B[1][1] 1.05
Anisotropic B[1][2] 1.3
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.1
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.9
c_dihedral_angle_d 21.3
c_angle_deg 1.8
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1015
Nucleic Acid Atoms 0
Heterogen Atoms 102
Solvent Atoms 105

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
MLPHARE model building
SCALEPACK data reduction
DENZO data collection