X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.2
Details CRYSTALS WERE GROWN BY THE HANGING DROP VAPOR DIFFUSION METHOD, pH 7.2, vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.71 α = 90
b = 65.45 β = 90
c = 38.03 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 291
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC -- 1995-11-09
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
-- -- -- -- --

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 15 8.0 0.07 -- -- 2.0 -- 9538 -- -- --
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 1.9 49.0 0.207 -- 2.6 -- --

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
THE ATOMIC COORDINATES OF THE NEW HIGH RESOLUTION REFINEMENT OF THE TRIGONAL FORM OF THE NATIVE ENZYME WERE USED AS THE STARTING MODEL (PDB CODE: 1MKT). 1.8 8.0 -- 2.0 -- 9538 -- 84.0 -- 0.196 0.196 -- --
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 1.88 -- -- -- 0.3 -- -- 46.0
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.6
x_bond_d 0.011
x_angle_deg 1.8
x_dihedral_angle_d 22.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 955
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 80

Software

Computing
Computing Package Purpose
R-AXIS IIC Data Reduction (intensity integration)
R-AXIS II Data Reduction (data scaling)
X-PLOR Structure Solution
X-PLOR Structure Refinement
Software
Software Name Purpose
X-PLOR refinement
X-PLOR model building
R-AXIS version: IIC data reduction
R-AXIS version: IIC data collection