X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 293.0
Details 100mM Citrate buffer, pH 5.5, 200mM NaCl, 1M NH4HPO4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 97.07 α = 90
b = 97.07 β = 90
c = 80.94 γ = 120
Symmetry
Space Group P 65

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2009-08-31
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 1.54 -- --

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
2.8 31.78 99.9 0.086 0.086 -- 22.7 10791 10791 -- -- 60.77
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)
2.8 2.95 100.0 0.385 0.385 2.0 22.6 1565

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 2.8 31.775 -- 1.36 -- 10762 544 99.93 -- 0.1923 0.1902 0.2326 --
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 2.8003 3.0819 2534 140 2534 0.2558 0.298 -- 100.0
X Ray Diffraction 3.0819 3.5274 2540 143 2540 0.2004 0.2709 -- 100.0
X Ray Diffraction 3.5274 4.4422 2556 131 2556 0.1657 0.2125 -- 100.0
X Ray Diffraction 4.4422 31.7771 2588 130 2588 0.1816 0.1997 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.2285
Anisotropic B[1][1] 2.6182
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.6182
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.2364
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.891
f_bond_d 0.006
f_plane_restr 0.003
f_dihedral_angle_d 13.147
f_chiral_restr 0.058
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2160
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 55

Software

Software
Software Name Purpose
MOSFLM data reduction
SCALA data scaling version: 3.2.25
PHASER phasing version: 2.3.0
PHENIX refinement version: 1.7.3_928
PDB_EXTRACT data extraction version: 3.11
CrystalClear data collection