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Crystal structure of wild-type IdmH, a putative polyketide cyclase from Streptomyces antibioticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6HNM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2 M calcium acetate, 0.1 MES, 18.6% (w/v) polyethylene glycol 8000
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.684 α = 90 b = 103.519 β = 91.63 c = 99.584 γ = 90
Symmetry Space Group P 1 21 1
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 2017-05-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.7 51.76 99.6 0.086 0.097 0.046 0.998 11.4 4.5 37144
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.82 99.5 0.655 1.4 4.3
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 6HNM 2.7 51.76 35294 1832 99.54 0.21232 0.2107 0.2149 0.24421 0.2469 RANDOM 69.399
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] 0.69 -2.64 2.23 -2.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 16.378 r_dihedral_angle_3_deg 12.688 r_long_range_B_refined 11.771 r_long_range_B_other 11.771 r_scangle_other 8.787 r_mcangle_it 8.398 r_mcangle_other 8.398 r_dihedral_angle_1_deg 5.971 r_scbond_it 5.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.58 r_dihedral_angle_4_deg 16.378 r_dihedral_angle_3_deg 12.688 r_long_range_B_refined 11.771 r_long_range_B_other 11.771 r_scangle_other 8.787 r_mcangle_it 8.398 r_mcangle_other 8.398 r_dihedral_angle_1_deg 5.971 r_scbond_it 5.828 r_scbond_other 5.828 r_mcbond_it 5.598 r_mcbond_other 5.596 r_angle_refined_deg 1.472 r_angle_other_deg 0.961 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10265 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement TRUNCATE data reduction Aimless data scaling PHASER phasing