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Crystal structure of beta-ketoacyl synthase from brucella melitensis with FOL 0758, (1-methyl-1h-indazol-3-yl) methanol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LRF native structure, 3LRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 290 MD PACT SCREEN, H12: 20% PEG 3350, 100MM BISTRISPROPANE PH 8.5, 200MM NA-MALONATE; CRYSTAL SOAKED 100MM MES PH 6.5, 250MM NACL, 30% PEG 3350, 10% GLYCEROL; BRABA.00113.A AT 22.9MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.25 45.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.07 α = 90 b = 83.62 β = 121.37 c = 73.64 γ = 90
Symmetry Space Group C 1 2 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 CCD ADSC QUANTUM Q315R 2010-04-02 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 1.25 4181 99.7 0.091 12.07 111226 -3 13.34
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) 1 1.25 1.28 99.1 0.404 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 MR THROUGHOUT native structure, 3LRF 1.25 41.81 111141 5562 99.8 0.113 0.112 0.1218 0.133 0.1406 RANDOM 7.42
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] 0.04 0.19 -0.03 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.148 r_dihedral_angle_4_deg 15.929 r_dihedral_angle_3_deg 11.459 r_dihedral_angle_1_deg 6.464 r_scangle_it 5.373 r_scbond_it 3.772 r_mcangle_it 2.535 r_mcbond_other 2.414 r_mcbond_it 1.777 r_rigid_bond_restr 1.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.148 r_dihedral_angle_4_deg 15.929 r_dihedral_angle_3_deg 11.459 r_dihedral_angle_1_deg 6.464 r_scangle_it 5.373 r_scbond_it 3.772 r_mcangle_it 2.535 r_mcbond_other 2.414 r_mcbond_it 1.777 r_rigid_bond_restr 1.735 r_angle_refined_deg 1.693 r_angle_other_deg 1.315 r_chiral_restr 0.119 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3012 Nucleic Acid Atoms Solvent Atoms 454 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling