X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 294.0
Details Reservoir: 1.5 M ammonium sulfate, 0.1 M Tris-HCl; protein drop: 7.5 microliter protein solution (8.7 mg/ml), 1 mM Na3VO4 plus 2.5 microliter reservoir solution. The peroxide complex was produced by soaking the crystals in mother liquor (2M ammonium sulfate, 0.1 M Tris-H2SO4, pH 8.0), containing 20 mM peroxide, for two hours and then flash cooled., VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 129.95 α = 90
b = 129.95 β = 90
c = 111.71 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Graphite monochromator 1996-06-23
Diffraction Radiation
Monochromator Protocol
Graphite SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.5418 -- --

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
2.24 33.84 88.3 0.118 0.114 -- 2.1 33853 29878 0.0 0.0 34.0
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)
2.24 2.34 40.2 0.297 0.293 1.2 2.0 3750

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
FOURIER SYNTHESIS 2.24 8.0 0.0 0.0 33172 29291 -- 88.3 -- -- 0.177 -- --
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 2.24 2.34 3685 -- -- 0.2972 -- -- --
X Ray Diffraction 2.34 2.46 3741 -- -- 0.2393 -- -- --
X Ray Diffraction 2.46 2.61 3705 -- -- 0.213 -- -- --
X Ray Diffraction 2.61 2.8 3713 -- -- 0.1978 -- -- --
X Ray Diffraction 2.8 3.07 3673 -- -- 0.1739 -- -- --
X Ray Diffraction 3.07 3.48 3676 -- -- 0.1517 -- -- --
X Ray Diffraction 3.48 4.27 3584 -- -- 0.1261 -- -- --
X Ray Diffraction 4.27 8.0 3514 -- -- 0.1601 -- -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 29.13
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.605
c_bond_d 0.011
c_dihedral_angle_d 23.17
c_improper_angle_d 1.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Resolution Cutoff (Low) 8.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4487
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 604

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (AGROVATA, ROTAVATA) Data Reduction (data scaling)
CCP4, SFCALC, FFT Structure Solution
X-PLOR 3.843 Structure Refinement
Software
Software Name Purpose
FFT model building
CCP4: version: SFCALC model building
X-PLOR version: 3.843 refinement