X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details ammonium sulfate, sodium citrate, pH 5.0, vapor diffusion : hanging drop, temperature 298.0K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 67.5 α = 90
b = 67.5 β = 90
c = 88.3 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
DIFFRACTOMETER WEISSENBERG -- 1998-10-18
Diffraction Radiation
Monochromator Protocol
SI (1 1 1) 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
1.5 100 86.9 0.026 -- -- 2.7 56679 56679 0.0 0.0 21.9
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)
1.5 1.54 67.1 0.359 -- -- 1.95 5037

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 1.5 100.0 -- 2.0 -- 50908 5771 86.9 -- 0.191 0.191 0.214 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 1.5 1.59 -- 832 6814 0.42 0.413 0.014 71.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 18.6
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 4.73
x_angle_deg 1.5
x_dihedral_angle_d 26.1
x_bond_d 0.013
x_mcbond_it 1.4
x_mcangle_it 1.88
x_scbond_it 3.07
x_improper_angle_d 0.87
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.15
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 6.0
Luzzati ESD (R-Free Set) 0.17
Luzzati Sigma A (R-Free Set) 0.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2672
Nucleic Acid Atoms 0
Heterogen Atoms 74
Solvent Atoms 334

Software

Software
Software Name Purpose
X-PLOR model building
X-PLOR refinement version: 98.1
DENZO data reduction
CCP4 data scaling version: (SCALA)
X-PLOR phasing