X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.6
Temperature 293.0
Details 20% (w/v) PEG 5000 monomethylethyl ether (MME), 200mM sodium citrate, 200mM sodium iodide, , pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.31 α = 90
b = 102.31 β = 90
c = 169.76 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-02-14
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.1 1.0 ALS 5.0.1

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
2.5 20 99.5 0.093 -- -- 10.5 18831 18831 0.0 0.0 --
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)
2.5 2.59 100.0 0.436 -- -- 10.5 1833

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 2.5 20.0 -- 0.0 18727 18727 968 99.26 -- 0.2242 0.2209 0.2891 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 2.5 2.564 -- 72 1096 0.301 0.421 -- 99.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.9526
Anisotropic B[1][1] -0.83
Anisotropic B[1][2] -0.42
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.83
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.25
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.006
r_chiral_restr 0.089
r_dihedral_angle_4_deg 16.089
r_dihedral_angle_3_deg 16.738
r_dihedral_angle_2_deg 33.569
r_dihedral_angle_1_deg 6.961
r_angle_refined_deg 1.393
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2885
Nucleic Acid Atoms 0
Heterogen Atoms 54
Solvent Atoms 43

Software

Computing
Computing Package Purpose
BOS Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
phaser Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
SCALEPACK data reduction