X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.25
Temperature 298.0
Details PEG 10,000, MES, glycerol, potassium chloride, beta-octylglucoside, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 96.14 α = 90
b = 112.37 β = 90
c = 162 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 ADSC QUANTUM 4 -- 2001-03-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-BM-C 1.000 APS 14-BM-C

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
2.2 30 97.7 0.089 0.089 -- 4.1 87015 82096 0.0 1.0 19.3
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)
2.2 2.28 91.3 0.398 0.398 3.4 2.7 8087

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 2.2 29.86 -- 0.0 81977 81977 8229 91.4 0.218 0.218 0.212 0.246 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 2.2 2.21 1221 137 11055 0.2832 0.3143 0.003 83.0
X Ray Diffraction 2.21 2.23 1218 124 -- 0.2503 0.2697 -- --
X Ray Diffraction 2.23 2.25 1300 143 -- 0.2655 0.2604 -- --
X Ray Diffraction 2.25 2.26 1376 156 -- 0.2488 0.2877 -- --
X Ray Diffraction 2.26 2.28 1366 134 -- 0.2527 0.3118 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 33.7
Anisotropic B[1][1] 0.45
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.2
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.65
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.05
c_scbond_it 2.09
c_mcangle_it 2.24
c_mcbond_it 1.35
c_improper_angle_d 0.83
c_dihedral_angle_d 22.3
c_angle_deg 1.3
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.27
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10291
Nucleic Acid Atoms 0
Heterogen Atoms 404
Solvent Atoms 543

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection