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Crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase ii from burkholderia vietnamiensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W0I pdb entry 1w0i modified with CCP4 program CHAINSAW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 290 QIAGEN JCSG-2 B5: 1M LICL, 100MM TRIS PH 8, 20% PEG 6000, BUVIA.00113.B.A1 PS01317 AT 21.5MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.02 39.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.82 α = 90 b = 101.32 β = 90 c = 131.18 γ = 90
Symmetry Space Group C 2 2 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 CCD RIGAKU SATURN 944+ 2012-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.9 50 99 0.075 0.075 18.14 6 30274 29974 -3 24.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 88 0.504 0.504 2.4 2.7 2236
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 1w0i modified with CCP4 program CHAINSAW 1.9 50 30274 29974 1517 99 0.15 0.15 0.148 0.1543 0.193 0.1982 RANDOM 16.1
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] 0.23 0.5 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.369 r_dihedral_angle_4_deg 18.625 r_dihedral_angle_3_deg 11.418 r_dihedral_angle_1_deg 6.028 r_angle_refined_deg 1.52 r_angle_other_deg 0.97 r_chiral_restr 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.369 r_dihedral_angle_4_deg 18.625 r_dihedral_angle_3_deg 11.418 r_dihedral_angle_1_deg 6.028 r_angle_refined_deg 1.52 r_angle_other_deg 0.97 r_chiral_restr 0.088 r_bond_refined_d 0.013 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it 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 3001 Nucleic Acid Atoms Solvent Atoms 325 Heterogen Atoms 1
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling