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 (pH 6.6) and 200mM sodium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101.88 α = 90
b = 101.88 β = 90
c = 169.16 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
-- -- -- 2008-02-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1 ALS 5.0.2

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
2.75 20 98.5 0.082 -- -- 7.6 -- 13736 -- -- --
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)
2.75 2.85 97.5 0.387 -- -- 5.7 1308

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 2.76 20.0 -- 0.0 -- 13653 680 98.05 -- 0.2246 0.2212 0.2884 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 2.76 2.83 -- 38 888 0.278 0.327 -- 93.91
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 54.768
Anisotropic B[1][1] 1.45
Anisotropic B[1][2] 0.73
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.45
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.18
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 2.851
r_scbond_it 1.667
r_mcangle_it 1.399
r_mcbond_it 0.751
r_gen_planes_refined 0.006
r_chiral_restr 0.09
r_dihedral_angle_4_deg 16.039
r_dihedral_angle_3_deg 18.435
r_dihedral_angle_2_deg 35.714
r_dihedral_angle_1_deg 7.047
r_angle_refined_deg 1.455
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2910
Nucleic Acid Atoms 0
Heterogen Atoms 38
Solvent Atoms 54

Software

Computing
Computing Package Purpose
HKL-2000 Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
phaser Structure Solution
REFMAC 5.5.0109 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.10 data extraction
REFMAC5 refinement
SCALEPACK data scaling