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Crystal structure of a type III polyketide synthase PKSIIINc from Neurospora crassa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CGZ PDB ENTRY 1CGZ and 1TED experimental model PDB 1TED PDB ENTRY 1CGZ and 1TED
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 295 PEG 8000, Isopropanol, Sodium acetate, HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.96 37.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.023 α = 90 b = 104.96 β = 90 c = 105.68 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 IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2007-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.58 25 97.6 0.091 4.4 24396 24396
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.58 2.67 88.2 0.387 2.24 3.5 2150
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1CGZ and 1TED 2.58 25 23093 23093 1229 97.99 0.21593 0.21346 0.2099 0.26016 RANDOM 32.068
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] 0.57 -1.45 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.499 r_dihedral_angle_3_deg 18.098 r_dihedral_angle_4_deg 16.782 r_dihedral_angle_1_deg 6.021 r_scangle_it 1.931 r_angle_refined_deg 1.361 r_scbond_it 1.172 r_mcangle_it 0.937 r_mcbond_it 0.522 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.499 r_dihedral_angle_3_deg 18.098 r_dihedral_angle_4_deg 16.782 r_dihedral_angle_1_deg 6.021 r_scangle_it 1.931 r_angle_refined_deg 1.361 r_scbond_it 1.172 r_mcangle_it 0.937 r_mcbond_it 0.522 r_nbtor_refined 0.304 r_nbd_refined 0.231 r_symmetry_hbond_refined 0.193 r_symmetry_vdw_refined 0.187 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5768 Nucleic Acid Atoms Solvent Atoms 413 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing