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 (8.7 mg/ml) in 5 mM Mops and 1 mM Na3VO4 plus 2.5 microliter reservoir solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 131.72 α = 90
b = 131.72 β = 90
c = 112.46 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 289
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE HENDRIX-LENTFER -- 1995-03-14
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
2.03 15.66 97.5 0.104 0.101 -- 2.4 46965 45791 0.0 0.0 29.01
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)
2.03 2.1 80.4 0.564 0.562 1.3 2.2 3649

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 2.03 8.0 2.0 2.0 44994 43870 -- 97.5 -- -- 0.1698 -- --
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 2.03 2.09 2677 -- -- 0.2784 -- -- 44.5
X Ray Diffraction 2.09 2.2 5632 -- -- 0.2344 -- -- --
X Ray Diffraction 2.2 2.33 5784 -- -- 0.2118 -- -- --
X Ray Diffraction 2.33 2.51 5847 -- -- 0.195 -- -- --
X Ray Diffraction 2.51 2.75 5969 -- -- 0.1831 -- -- --
X Ray Diffraction 2.75 3.13 6009 -- -- 0.1632 -- -- --
X Ray Diffraction 3.13 3.86 6003 -- -- 0.1398 -- -- --
X Ray Diffraction 3.86 8.0 5949 -- -- 0.153 -- -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 30.85
Anisotropic B[1][1] 3.49
Anisotropic B[1][2] 3.18
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 3.49
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -6.99
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.497
c_dihedral_angle_d 22.86
c_angle_deg 1.601
c_bond_d 0.011
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4477
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 456

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (AGROVATA, ROTAVATA) Data Reduction (data scaling)
CCP4, SFCALC, FFT Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
FFT model building
CCP4: version: SFCALC model building