X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.5
Details 12% PEG 4K, 100 MM MGCL2, 100 MM ACETATE BUFFER, PH 4.5

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 78.45 α = 90
b = 78.45 β = 90
c = 159.1 γ = 120
Symmetry
Space Group P 32 1 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE FUJI MIRRORS 1994-07
Diffraction Radiation
Monochromator Protocol
SI(111) --
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
2.75 15 96.9 0.071 -- -- 3.2 -- 14428 -- -3.0 30.8
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)
2.75 3.0 97.2 0.314 -- 2.3 3.0 --

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 2.75 6.0 -- 0.0 -- 13095 1323 97.9 -- 0.246 0.246 0.325 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 2.75 2.86 -- 162 1442 0.373 0.444 0.036 96.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 47.6
Anisotropic B[1][1] -10.0
Anisotropic B[1][2] -10.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -10.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.0
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 9.35
x_scbond_it 5.52
x_mcangle_it 5.98
x_mcbond_it 3.53
x_improper_angle_d 1.31
x_bond_d 0.015
x_angle_deg 1.6
x_dihedral_angle_d 24.6
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.39
Luzzati Sigma A (Observed) 0.61
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.53
Luzzati Sigma A (R-Free Set) 0.72
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3108
Nucleic Acid Atoms 0
Heterogen Atoms 28
Solvent Atoms 22

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (AGROVATA, ROTAVATA) Data Reduction (data scaling)
AMORE Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
AMORE model building
ROTAVATA/AGROVATA data reduction
DENZO data collection