X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Details THE PROTEIN WAS CRYSTALLIZED IN HANGING DROPS USING 3M (NH4)H2P04 AS THE PRECIPITANT (PH 5.6). 50 MM HEPES, PH 8.0, 10 MM MGSO4, 10 MM DTT AND 5 MM GDP WAS THE BUFFER, vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 77.19 α = 90
b = 77.19 β = 90
c = 143.61 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 278
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU MIRRORS 1996-04
Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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
2.8 15 93.1 0.059 -- -- 2.8 -- 10403 -- -- --
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)
2.8 2.93 95.2 0.237 -- -- -- --

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
DIFFERENCE FOURIER 2.8 8.0 -- 1.0 -- 10063 1050 93.8 -- 0.189 0.189 0.25 SAME AS IN 1GIT
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 2.8 2.92 -- 124 1088 0.27 0.306 -- 91.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 39.4
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.4
x_angle_deg 1.65
x_dihedral_angle_d 23.5
x_bond_d 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2539
Nucleic Acid Atoms 0
Heterogen Atoms 33
Solvent Atoms 5

Software

Software
Software Name Purpose
X-PLOR model building version: 3.1
X-PLOR refinement version: 3.1
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing version: 3.1