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 = 96.76 α = 90
b = 96.76 β = 90
c = 80.96 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++ -- 2009-09-10
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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 37.22 100.0 0.079 0.079 -- 12.5 10721 10721 -- -- 64.3
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 0.403 0.403 1.9 12.5 1555

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 2.801 31.674 -- 1.37 10693 10689 541 99.98 -- 0.1751 0.1726 0.2236 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 2.8015 3.0832 2512 143 2512 0.2675 0.3782 -- 100.0
X Ray Diffraction 3.0832 3.5289 2517 137 2517 0.1687 0.239 -- 100.0
X Ray Diffraction 3.5289 4.444 2532 131 2532 0.1487 0.1988 -- 100.0
X Ray Diffraction 4.444 31.6758 2587 130 2587 0.1625 0.1805 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 44.7889
Anisotropic B[1][1] 2.325
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.325
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.6499
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.004
f_dihedral_angle_d 13.792
f_bond_d 0.005
f_chiral_restr 0.059
f_angle_d 0.777
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2140
Nucleic Acid Atoms 0
Heterogen Atoms 39
Solvent Atoms 60

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