X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.75
Details 20% PEG 4000, 7% EG, 80MM A.S, 200MM AMM.ACETATE, 50MM NA.ACETATE PH 4.75

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 112.25 α = 90
b = 112.25 β = 90
c = 99.72 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE FUJI -- --
Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A -- NSLS X4A

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
1.9 -- 95.7 -- 0.05 -- 4.12 -- 48139 -- 0.0 25.1
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)
1.9 1.99 96.6 -- 0.27 2.5 -- --

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
MOLECULAR REPLACEMENT 1.9 10.0 -- 0.0 -- 47865 2410 95.7 -- 0.214 0.214 0.263 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 1.9 1.99 -- 293 5627 0.357 0.392 0.023 96.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 30.9
Anisotropic B[1][1] -4.22
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -4.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.43
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 2.67
x_scbond_it 1.65
x_mcangle_it 2.53
x_mcbond_it 1.47
x_improper_angle_d 1.18
x_bond_d 0.009
x_angle_deg 2.0
x_dihedral_angle_d 25.1
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.34
Luzzati Resolution Cutoff (Low) 10.0
Luzzati ESD (R-Free Set) 0.29
Luzzati Sigma A (R-Free Set) 0.32
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3129
Nucleic Acid Atoms 0
Heterogen Atoms 42
Solvent Atoms 369

Software

Computing
Computing Package Purpose
HKL, DENZO Data Reduction (intensity integration)
CCP4 (AGROVATA, SCALA) Data Reduction (data scaling)
X-PLOR Structure Solution
X-PLOR Structure Refinement
Software
Software Name Purpose
X-PLOR refinement
X-PLOR model building
AGROVATA data reduction
SCALA data reduction
DENZO data collection
HKL data collection