X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 290.0
Details 0.1 M HEPES PH 7.5, 1.5-1.7 M LISO4 AND 10 MM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 107.45 α = 90
b = 107.45 β = 90
c = 53.42 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ -- 2010-06-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
2.3 50 99.8 0.118 -- -- 7.0 -- 15727 -- -- --
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)
2.3 2.34 100.0 0.872 -- -- 6.3 764

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 2.3 26.862 -- 0.98 -- 15618 785 99.17 -- 0.2099 0.2071 0.2611 --
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 2.3 2.4467 -- 115 2458 0.2607 0.3379 -- 99.0
X Ray Diffraction 2.4467 2.6355 -- 130 2448 0.2574 0.3317 -- 100.0
X Ray Diffraction 2.6355 2.9004 -- 151 2447 0.2366 0.333 -- 100.0
X Ray Diffraction 2.9004 3.3195 -- 137 2471 0.2236 0.2921 -- 99.0
X Ray Diffraction 3.3195 4.1796 -- 121 2465 0.2038 0.2675 -- 98.0
X Ray Diffraction 4.1796 26.8641 -- 131 2544 0.1717 0.1853 -- 99.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 50.1128
Anisotropic B[1][1] -0.7151
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.7151
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.4302
RMS Deviations
Key Refinement Restraint Deviation
f_angle_d 0.797
f_bond_d 0.007
f_dihedral_angle_d 13.512
f_plane_restr 0.006
f_chiral_restr 0.046
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2356
Nucleic Acid Atoms 0
Heterogen Atoms 75
Solvent Atoms 105

Software

Software
Software Name Purpose
HKL data processing
PHASER phasing version: 2.1.4
PHENIX refinement version: 1.6.4_486
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
HKL data reduction
HKL data scaling