X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details PROTEIN WAS RESUSPENDED IN 30 MM PHOSPHATE BUFFER, PH 7.0, DEOXYGENATED AND CONCENTRATED TO 160 MG/ML. PROTEIN WAS CRYSTALLIZED IN AN ANAEROBIC CHAMBER IN TUBE CONTAINING 10 UL PROTEIN SOLUTION, 5 UL CITRATE BUFFER (PH 4.0), AND 4UL OF 33% PEG 8K.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 62.95 α = 90
b = 81.28 β = 90
c = 111.35 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC COLLIMATOR 1996-03-01
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
2 100 89.2 -- 0.076 -- 3.2 -- 35597 -- 2.0 13.8
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)
2.0 2.09 70.3 -- 0.371 -- -- --

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 2.0 20.0 -- 2.0 -- 33002 3354 84.6 -- 0.198 0.198 0.264 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 2.0 2.09 -- 346 3038 0.228 0.27 0.015 70.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 14.0
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 8.84
x_scbond_it 13.55
x_mcangle_it 2.25
x_mcbond_it 1.54
x_improper_angle_d 1.68
x_bond_d 0.012
x_angle_deg 1.6
x_dihedral_angle_d 19.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.11
Luzzati Resolution Cutoff (Low) 8.0
Luzzati ESD (R-Free Set) 0.31
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4394
Nucleic Acid Atoms 0
Heterogen Atoms 172
Solvent Atoms 369

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 3.843 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.843 refinement
AMORE model building
SCALEPACK data reduction
DENZO data collection