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Crystal structure of 3-Ketoacyl-(acyl-carrier-protein) reductase from Burkholderia pseudomallei at 2.05 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Q7B pdb entry 1q7b, side chains modified by ccp4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 290 PROPLEX-96 SCREEN C5: 100MM TRIS, 20% PEG 4000, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.08 40.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.62 α = 90 b = 89.9 β = 90 c = 120.24 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 CCD RIGAKU SATURN 944 2008-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 2.05 20 89.1 0.06 17 5.3 59670 53192 -3 39.59
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 2.05 2.1 84.5 0.48 3.2 2.2 4349
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 1q7b, side chains modified by ccp4 program chainsaw 2.05 19.68 52958 52958 2690 88.9 0.211 0.211 0.208 0.21 0.268 0.2688 RANDOM 24.48
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] 0.03 -0.21 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.43 r_dihedral_angle_4_deg 15.092 r_dihedral_angle_3_deg 14.649 r_dihedral_angle_1_deg 6.304 r_scangle_it 3.773 r_scbond_it 2.316 r_angle_refined_deg 1.498 r_mcangle_it 1.485 r_angle_other_deg 0.949 r_mcbond_it 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.43 r_dihedral_angle_4_deg 15.092 r_dihedral_angle_3_deg 14.649 r_dihedral_angle_1_deg 6.304 r_scangle_it 3.773 r_scbond_it 2.316 r_angle_refined_deg 1.498 r_mcangle_it 1.485 r_angle_other_deg 0.949 r_mcbond_it 0.83 r_mcbond_other 0.191 r_chiral_restr 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 6889 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling