X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Details PROTEIN WAS CRYSTALLIZED AT 17 MG/ML FROM 0.42 M NAH(2)PO(4), 1.70 M K(2)HPO(4), 10 MM BES, 6 MM DTT, 0.035% NAN(3), 29% ETHYLENE GLYCOL.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 157.68 α = 90
b = 157.68 β = 90
c = 90.93 γ = 90
Symmetry
Space Group P 42 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PRINCETON 2K BENT FOCUSING MIRRORS 1997-01
Diffraction Radiation
Monochromator Protocol
SI(111) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON CHESS BEAMLINE F1 -- CHESS F1

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
2.3 20 83.5 -- 0.108 -- 5.95 -- 42831 -- 1.0 25.2
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)
2.3 2.4 65.0 -- 0.39 1.9 -- --

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 2.3 20.0 -- 1.0 -- 42831 4277 83.5 -- 0.225 0.225 0.254 SHELLS
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 2.3 2.4 -- 292 3853 0.353 0.395 0.023 65.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 61.6
Anisotropic B[1][1] -3.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -3.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 6.44
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 11.74
x_scbond_it 7.92
x_mcangle_it 7.13
x_mcbond_it 4.75
x_improper_angle_d 1.46
x_bond_d 0.012
x_angle_deg 1.6
x_dihedral_angle_d 25.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.31
Luzzati Sigma A (Observed) 0.44
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.48
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5698
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 469

Software

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