X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Lipidic Cubic Phase
pH 8
Temperature 294.0
Details 29-31% Peg 400,100 mM Tris pH 8.0. 0.2 M Na Malonate,200 uM TAK-875
Method Lipidic Cubic Phase
pH 7.2
Temperature 294.0
Details 39.8 % Peg 400, 100 mM Bis-Tris-Propane pH 7.2, 0.1 Ammonium Phosphate (monobasic), 200 uM TAK-875

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 101 α = 90
b = 61.74 β = 108.9
c = 105.7 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2012-06-05
CCD ADSC QUANTUM 315r -- 2012-05-22
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Si(220) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.3 0.976 ALS 5.0.3
SYNCHROTRON APS BEAMLINE 23-ID-B 1.0 APS 23-ID-B

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
2.33 100 98.2 -- 0.12 4.538 5.0 26022 26022 -- -- --
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)
2.33 2.46 90.0 0.623 0.623 1.0 3.4 3506

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 2.332 30.0 -- 0.0 -- 25947 1312 97.85 -- 0.1999 0.1981 0.2331 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 2.332 2.392 -- 67 1493 0.267 0.332 -- 79.51
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 48.541
Anisotropic B[1][1] 2.17
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -0.24
Anisotropic B[2][2] -0.55
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.18
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_angle_refined_deg 1.118
r_bond_other_d 0.001
r_chiral_restr 0.062
r_dihedral_angle_2_deg 35.679
r_gen_planes_other 0.001
r_dihedral_angle_1_deg 4.978
r_bond_refined_d 0.007
r_mcangle_it 1.894
r_mcbond_other 1.103
r_angle_other_deg 0.743
r_dihedral_angle_4_deg 15.969
r_dihedral_angle_3_deg 16.263
r_mcbond_it 1.104
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms --
Nucleic Acid Atoms --
Heterogen Atoms 127
Solvent Atoms 90

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.21
MOLREP phasing version: 10.2.35
REFMAC refinement version: 5.8.0049
PDB_EXTRACT data extraction version: 3.14
Coot model building version: 0.7