X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 6.3 mg/ml enzyme, 5.5% PEG 3350, 9 mM imidazole; over a reservoir of 24% PEG 3350. Crystal was reacted with 9 mM DVR-II-41s in 15 mM imidazole/28% PEG 3350, pH 7.0 for 3 hr. and then soaked in an identical solution for 35 min. The crystal was soaked in a cryo-protectant solution of 25% glycerol/20 mM HEPES (pH 7)/24% PEG for 2 min. prior to cryo-freezing., VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77 α = 90
b = 69 β = 90
c = 62.5 γ = 90
Symmetry
Space Group P 21 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-02-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE A1 0.935 CHESS A1

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
1.6 50 66.1 0.087 -- -- 3.2 -- 29788 -- -3.0 10.8
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)
1.6 2.02 32.2 0.31 -- 2.7 1.7 7159

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 1.6 100.0 0.0 0.0 28503 28503 1672 100.0 0.183 0.183 0.181 0.208 random
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model restrained, isotropic
Mean Isotropic B 14.7
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.47
c_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2783
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 315

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
AMORE model building
CNS version: 1.0 refinement