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 OVER A PERIOD OF ELEVEN MONTHS USING THE HANGING DROP VAPOR DIFFUSION METHOD BY EMPLOYING THE CONDITIONS 5 (MICRO)L OF THE PROTEIN (20 MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2.5 (MICRO)L OF 75% MPD IN THE DROPLET. THE RESERVOIR CONTAINED (55%) OF MPD., vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 46.87 α = 90
b = 46.87 β = 90
c = 103.04 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 -- 1996-08-02
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
-- R-AXIS IIC -- -- --

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
1.9 10 92.0 0.061 -- -- 5.0 -- 9912 -- -- --
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)
1.9 1.99 79.0 0.225 -- -- -- --

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 HIGH RESOLUTION ATOMIC COORDINATES OF THE WILD TYPE (PDB ENTRY 1MKT) WERE USED AS THE STARTING MODEL FOR FURTHER REFINEMENT 1.9 10.0 -- 2.0 -- 9903 688 92.0 -- 0.198 0.198 0.277 X-PLOR METHOD
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 1.97 -- 53 710 0.309 0.329 -- 72.0
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.2
x_bond_d 0.013
x_angle_deg 1.73
x_dihedral_angle_d 23.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.21
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 958
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 70

Software

Computing
Computing Package Purpose
R-AXIS IIC Data Reduction (intensity integration)
R-AXIS II Data Reduction (data scaling)
X-PLOR 3.1 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR version: 3.1 model building
R-AXIS version: IIC data reduction
R-AXIS version: IIC data collection