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 FROM DROPLETS CONTAINING 5 (MICRO)L OF THE MUTANT PROTEIN (15MG/ML) 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2 (MICRO)L OF 75% MPD AND (50%) OF MPD IN THE RESERVOIR, vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 47.08 α = 90
b = 47.08 β = 90
c = 102.37 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 291
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC -- 1995-12-01
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
1.82 15 8.0 0.069 -- -- 2.0 -- 7346 -- -- --
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)
1.82 2.0 29.0 0.194 -- 1.72 -- --

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 ENTRY 1MKT). 1.9 8.0 -- 2.0 -- 6809 -- 64.0 -- 0.186 0.186 -- --
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 1.9 1.99 -- -- -- 0.312 -- -- 32.0
RMS Deviations
Key Refinement Restraint Deviation
x_dihedral_angle_d 23.1
x_angle_deg 2.7
x_improper_angle_d 1.2
x_bond_d 0.015
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 77

Software

Computing
Computing Package Purpose
R-AXIS IIC Data Reduction (intensity integration)
R-AXIS II Data Reduction (data scaling)
X-PLOR 3.0 Structure Solution
X-PLOR 3.0 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.0 model building
X-PLOR version: 3.0 refinement
R-AXIS version: IIC data collection
R-AXIS version: IIC data reduction