X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 293.0
Details 10% PEG 4000 0.1 M SODIUM CITRATE 20% 2-PROPANOL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.83 α = 90
b = 41.83 β = 90
c = 84.82 γ = 120
Symmetry
Space Group P 3 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS -- 1999-03-24
Diffraction Radiation
Monochromator Protocol
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 1.1197, 1.1393, 1.1403, 1.1399 NSLS X4A

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
1.5 35 93.8 0.048 -- -- 6.5 14503 13604 0.0 -3.0 21.6
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)
1.5 1.55 86.8 0.235 -- 4.5 6.1 --

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
-- 1.5 10.0 0.0 0.0 14322 13549 1362 94.6 0.214 0.214 0.214 0.245 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 1.5 1.59 -- 219 2008 0.233 0.27 0.018 96.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.7
Anisotropic B[1][1] 3.61
Anisotropic B[1][2] 1.74
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.61
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.22
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.676
c_scbond_it 1.853
c_mcangle_it 1.503
c_mcbond_it 0.956
c_improper_angle_d 1.0
c_bond_d 0.012
c_angle_deg 1.5
c_dihedral_angle_d 15.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.09
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.12
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 515
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 150

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE Structure Solution
CNS 0.5 Structure Refinement
Software
Software Name Purpose
CNS version: 0.5 refinement
MLPHARE model building
SCALEPACK data reduction
DENZO data collection