☰ Navigation Tabs
Co-crystal structures of PP5 in complex with 5-methyl-7-oxabicyclo[2.2.1]heptane-2,3-dicarboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S95 PDB entry 1s95
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 289 25% MPD, 6% PEG, 10 mM Tris, pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.97 37.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.858 α = 88.15 b = 80.52 β = 87.33 c = 91.165 γ = 86.71
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 2014-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
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 2 91.03 97.9 0.086 0.074 0.986 11.7 2.4 76635
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 2 2.11 96.8 0.505 0.421 0.64 2.1 2.4 11083
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1s95 2 91.03 72774 3848 97.86 0.20593 0.20438 0.2051 0.23517 0.2362 RANDOM 33.285
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] -0.38 -0.74 0.54 1.56 0.01 -1.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.07 r_dihedral_angle_3_deg 12.614 r_dihedral_angle_4_deg 12.354 r_dihedral_angle_1_deg 5.602 r_angle_refined_deg 1.094 r_chiral_restr 0.075 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.07 r_dihedral_angle_3_deg 12.614 r_dihedral_angle_4_deg 12.354 r_dihedral_angle_1_deg 5.602 r_angle_refined_deg 1.094 r_chiral_restr 0.075 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10032 Nucleic Acid Atoms Solvent Atoms 283 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHENIX phasing PDB_EXTRACT data extraction XDS data reduction