X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.8
Details THE PROTEIN WAS CONCENTRATED TO 12 MG/ML IN THE PRESENCE OF 5MM LYSINE AND WAS CRYSTALLISED FROM 0.1 M PIPES PH 6.8, 0.5 M LICL, 20% PEG 4K, 17% GLYCEROL; THEN, A SMALL AMOUNT OF A SOLUTION CONTAINING ATP AND MGCL2 WAS ADDED TO THE DROP TO GET A FINAL CONCENTRATION OF ABOUT 5 MM.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 143.1 α = 90
b = 143.1 β = 90
c = 176.1 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRROR 1995-06-15
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 -- EMBL/DESY, HAMBURG X11

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
2.4 15 98.2 0.086 0.086 -- 8.0 -- 41908 -- -- --
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)
2.4 2.44 94.1 0.204 0.204 4.1 3.6 --

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
OTHER 2.4 15.0 -- 0.0 -- 40860 1639 98.0 -- 0.186 0.186 0.267 RANDOM
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 2.4 2.51 -- 209 4675 0.267 0.292 0.02 96.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 6.3
x_scbond_it 4.2
x_mcangle_it 3.4
x_mcbond_it 2.26
x_improper_angle_d 1.66
x_bond_d 0.007
x_angle_deg 1.6
x_dihedral_angle_d 17.0
Coordinate Error
Parameter Value
Luzzati Resolution Cutoff (Low) 20.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3834
Nucleic Acid Atoms 0
Heterogen Atoms 85
Solvent Atoms 337

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 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