X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.4
Temperature 289.0
Details 3.5% 1,2,3 -heptanetriol, 2% dioxane, 0.1% LDAO, 1M potassium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 140.13 α = 90
b = 140.13 β = 90
c = 186.03 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MAR CCD 165 mm -- 2011-10-24
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8123 EMBL/DESY, Hamburg X13

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
2.9 28.9 96.5 0.092 -- -- 4.61 47384 45707 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)
2.9 3.0 90.2 0.664 -- 2.3 4.55 --

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 2.9 28.9 -- 0.0 45707 43421 2286 100.0 0.212 0.20626 0.20394 0.25063 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 2.9 2.975 -- 154 2912 0.354 0.418 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 69.052
Anisotropic B[1][1] 1.39
Anisotropic B[1][2] 0.69
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.08
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 5.639
r_dihedral_angle_3_deg 17.35
r_dihedral_angle_2_deg 33.879
r_chiral_restr 0.086
r_mcbond_it 0.468
r_angle_refined_deg 1.72
r_scbond_it 1.056
r_scangle_it 1.862
r_gen_planes_refined 0.006
r_dihedral_angle_4_deg 18.743
r_mcangle_it 0.896
r_bond_refined_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6484
Nucleic Acid Atoms 0
Heterogen Atoms 683
Solvent Atoms 49

Software

Software
Software Name Purpose
XDS data scaling
PHASER phasing
REFMAC refinement version: 5.5.0109
XDS data reduction