X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4
Details 10MG/ML PROTEIN IN 0.1M TRIS-CL PH 7.5 MIX 2 MICROLITER OF PROTEIN SOLUTION WITH 2 MICROLITER OF WELL SOLUTION IN A HANGING DROP EXPERIMENT. THE WELL CONTAINS 0.1M NA-ACETATE PH 4.0, 12% PEG 35000, 0.3M CACL2

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.2 α = 90
b = 106.84 β = 99.42
c = 101.39 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARRESEARCH -- 2000-01-15
Diffraction Radiation
Monochromator Protocol
-- 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
2.37 20 98.9 0.083 -- -- 4.94 -- 73996 -- -- 20.4
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)
2.37 2.45 95.1 0.214 -- 4.915 4.14 --

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 2.37 20.0 -- 0.0 -- 73042 3683 98.8 -- 0.1772 0.1772 0.2323 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 2.37 2.52 -- 565 11242 0.204 0.279 0.012 96.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.6
Anisotropic B[1][1] -3.94
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -5.79
Anisotropic B[2][2] 0.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 3.23
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.681
c_scbond_it 1.796
c_mcangle_it 1.956
c_mcbond_it 1.164
c_improper_angle_d 0.86
c_bond_d 0.007
c_angle_deg 1.5
c_dihedral_angle_d 22.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.19
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.31
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 14846
Nucleic Acid Atoms 0
Heterogen Atoms 144
Solvent Atoms 1094

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMORE model building