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Pimaricin type I PKS thioesterase domain (holo Pim TE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M HEPES pH 7.5, 1.5M Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 4.37 71.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.449 α = 90 b = 95.449 β = 90 c = 102.708 γ = 120
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 2017-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97774 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.4 82.66 100 0.097 0.102 0.032 5.8 10.2 20938
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.44 100 1.238 1.309 0.425 0.847 9.4
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 7VO4 2.4 82.66 19907 992 99.94 0.203 0.2015 0.2171 0.2319 0.2427 RANDOM 45.253
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] 0.21 0.11 0.21 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.951 r_dihedral_angle_4_deg 23.208 r_dihedral_angle_3_deg 19.716 r_dihedral_angle_1_deg 7.047 r_angle_refined_deg 2.058 r_angle_other_deg 1.15 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.951 r_dihedral_angle_4_deg 23.208 r_dihedral_angle_3_deg 19.716 r_dihedral_angle_1_deg 7.047 r_angle_refined_deg 2.058 r_angle_other_deg 1.15 r_chiral_restr 0.112 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2074 Nucleic Acid Atoms Solvent Atoms 53 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction PHASER phasing