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 5 MM 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 AMP-PCP AND MGCL2 WAS ADDED TO THE DROP TO GET A FINAL CONCENTRATION OF ABOUT 5 MM.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 142.02 α = 90
b = 142.02 β = 90
c = 175.39 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 ELETTRA BEAMLINE 5.2R -- ELETTRA 5.2R

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
2.43 25 84.7 0.065 0.065 -- 3.6 -- 33781 -- -- --
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)
2.43 2.54 65.1 0.099 0.099 6.3 3.1 --

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
MOLECULAR REPLACEMENT 2.43 12.0 -- 0.0 -- 33420 1347 84.7 -- 0.176 0.176 0.228 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 2.43 2.54 -- 127 2895 0.257 0.329 0.03 65.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
RMS Deviations
Key Refinement Restraint Deviation
x_mcangle_it 3.66
x_dihedral_angle_d 20.4
x_angle_deg 1.4
x_improper_angle_d 2.4
x_bond_d 0.006
x_scbond_it 4.52
x_scangle_it 6.9
x_mcbond_it 2.39
Coordinate Error
Parameter Value
Luzzati Resolution Cutoff (Low) 20.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3816
Nucleic Acid Atoms 0
Heterogen Atoms 80
Solvent Atoms 306

Software

Software
Software Name Purpose
X-PLOR refinement version: 3.1
MOSFLM data reduction
CCP4 data scaling
X-PLOR phasing version: 3.1