X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 3.5
Details CRYSTALS GREW AS NEEDLES FROM 10MG/ML HLA-DR1 / PEPTIDE COMPLEX, 15% PEG 4000, 100MM GLYCINE, PH 3.5, AT ROOM TEMPERATURE, OVER ONE WEEK.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 134.51 α = 90
b = 134.32 β = 104.82
c = 131.23 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 98
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE FUJI -- 1995-02
Diffraction Radiation
Monochromator Protocol
-- --
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
2.45 20 85.0 -- 0.07 -- 2.1 -- 73538 -- 2.0 37.2
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)
2.45 2.57 70.0 -- 0.331 4.4 1.8 --

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 2.45 6.0 -- 2.0 -- 68842 6884 89.0 -- 0.216 0.216 0.279 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 2.45 2.57 -- 770 6930 0.319 0.354 -- 70.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 40.8
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 0.25
x_scbond_it 0.2
x_mcangle_it 0.2
x_mcbond_it 0.15
x_bond_d 0.016
x_angle_deg 2.6
x_dihedral_angle_d 26.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.4
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12486
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 152

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
SCALEPACK data reduction
DENZO data collection