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Crystal structure of beta-ketoacyl synthase from brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DD8 pdb entry 1dd8 modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 MD PACT SCREEN, H12: 20% PEG 3350, 100MM BISTRISPROPANE PH 8.5, 200MM NA-MALONATE; BRABA.00113.A AT 22.9MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.21 44.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.48 α = 90 b = 83.27 β = 120.97 c = 72.87 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 RIGAKU SATURN 944+ 2010-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 1.6 50 98.1 0.039 34.19 8.1 52414 51415 -3 18.47
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) 1.6 1.64 91.8 0.327 4.9 4.8 3853
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 (All) 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 pdb entry 1dd8 modified with CCP4 program CHAINSAW 1.6 50 52414 51415 2613 98.4 0.13 0.13 0.129 0.138 0.158 0.165 RANDOM 9.1
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] -0.09 0.05 0.29 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.987 r_dihedral_angle_4_deg 15.052 r_dihedral_angle_3_deg 11.792 r_dihedral_angle_1_deg 6.087 r_scangle_it 3.537 r_scbond_it 2.167 r_angle_refined_deg 1.468 r_mcangle_it 1.291 r_angle_other_deg 0.879 r_mcbond_it 0.742
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.987 r_dihedral_angle_4_deg 15.052 r_dihedral_angle_3_deg 11.792 r_dihedral_angle_1_deg 6.087 r_scangle_it 3.537 r_scbond_it 2.167 r_angle_refined_deg 1.468 r_mcangle_it 1.291 r_angle_other_deg 0.879 r_mcbond_it 0.742 r_mcbond_other 0.219 r_chiral_restr 0.089 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3091 Nucleic Acid Atoms Solvent Atoms 493 Heterogen Atoms 1
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling