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Crystal structure of Autotaxin (ENPP2) with 7-alpha-hydroxycholesterol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XR9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG 3350, 0.1M ammonium iodide 0.3M sodium thiocyanate, 23.5mg/ml heparin sulfate
Crystal Properties Matthews coefficient Solvent content 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.671 α = 98.72 b = 63.482 β = 105.8 c = 70.715 γ = 99.97
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2011-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97935 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1 1.6 44.02 92.1 0.065 0.061 0.997 6.7 2 105202 29.61
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 88.9 0.868 0.815 0.437 0.8 1.9 5091
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2xr9 1.6 44.02 99938 5262 92.11 0.1725 0.1713 0.1964 0.203 RANDOM 28.789
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.22 -0.02 0.33 0.21 0.1 -0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.694 r_dihedral_angle_4_deg 16.806 r_dihedral_angle_3_deg 12.18 r_sphericity_bonded 11.517 r_dihedral_angle_1_deg 6.214 r_mcangle_it 2.295 r_mcbond_it 1.491 r_mcbond_other 1.467 r_angle_refined_deg 1.45 r_angle_other_deg 0.955
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.694 r_dihedral_angle_4_deg 16.806 r_dihedral_angle_3_deg 12.18 r_sphericity_bonded 11.517 r_dihedral_angle_1_deg 6.214 r_mcangle_it 2.295 r_mcbond_it 1.491 r_mcbond_other 1.467 r_angle_refined_deg 1.45 r_angle_other_deg 0.955 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6431 Nucleic Acid Atoms Solvent Atoms 528 Heterogen Atoms 158
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling XDS data reduction PHASER phasing Coot model building