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Crystal structure of type III polyketide synthase from Mycobacterium marinum - P 21 21 21 Space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7CB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 1 M Potassium Sodium tartrate
200 mM Sodium chloride
100 mM Imidazole; pH 8.0
Crystal Properties Matthews coefficient Solvent content 1.97 37.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.732 α = 90 b = 99.518 β = 90 c = 126.707 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 S 6M 2018-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97735 ESRF ID29
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 2.419 78.264 92.1 0.107 0.117 0.046 0.997 9.4 6.2 19645 55.9
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 2.419 2.685 57 0.618 0.752 0.419 0.719 1.4 2.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7CB3 2.419 78.264 19644 962 71.027 0.206 0.2038 0.2083 0.2582 0.2594 51.418
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] -0.119 -0.027 0.145
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.264 r_dihedral_angle_3_deg 16.359 r_dihedral_angle_4_deg 12.654 r_lrange_it 8.332 r_lrange_other 8.331 r_dihedral_angle_1_deg 6.256 r_scangle_it 4.465 r_scangle_other 4.464 r_mcangle_it 3.722 r_mcangle_other 3.721
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.264 r_dihedral_angle_3_deg 16.359 r_dihedral_angle_4_deg 12.654 r_lrange_it 8.332 r_lrange_other 8.331 r_dihedral_angle_1_deg 6.256 r_scangle_it 4.465 r_scangle_other 4.464 r_mcangle_it 3.722 r_mcangle_other 3.721 r_scbond_it 2.736 r_scbond_other 2.735 r_mcbond_it 2.281 r_mcbond_other 2.281 r_angle_refined_deg 1.339 r_angle_other_deg 1.171 r_nbd_other 0.252 r_nbd_refined 0.192 r_symmetry_nbd_other 0.179 r_symmetry_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.152 r_symmetry_nbd_refined 0.138 r_xyhbond_nbd_refined 0.113 r_ncsr_local_group_1 0.083 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.07 r_chiral_restr 0.048 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5382 Nucleic Acid Atoms Solvent Atoms 32 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling SHELXDE phasing