X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 295.7
Details HANGING DROP, PEG 4000, SODIUM ACETATE, AMMONIUM ACETATE, TES, pH 6.00, VAPOR DIFFUSION, HANGING DROP, temperature 295.7K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 63.65 α = 90
b = 63.65 β = 90
c = 262.9 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE WEISSENBERG -- 1998-12-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6B -- PHOTON FACTORY BL-6B

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
2.5 37.5 98.2 0.046 -- -- 3.4 -- 19281 -- -- 36.1
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)
2.5 2.63 98.2 0.064 -- 9.8 3.5 --

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
MIR 2.5 20.0 -- 2.0 -- 19063 1883 97.0 -- 0.223 0.223 0.316 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 2.5 2.66 -- 308 2758 0.294 0.428 0.024 96.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 28.5
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 5.87
x_scbond_it 4.5
x_mcangle_it 4.25
x_mcbond_it 2.86
x_improper_angle_d 0.8
x_bond_d 0.01
x_angle_deg 1.6
x_dihedral_angle_d 26.7
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.3
Luzzati Sigma A (Observed) 0.26
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.44
Luzzati Sigma A (R-Free Set) 0.43
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4296
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 284

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
SHARP, MLPHARE Structure Solution
X-PLOR 98.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 98.1 refinement
MLPHARE model building
SHARP model building