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Structure of mitochondrial beta-ketoacyl synthase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W0I PDB ENTRY 1W0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1 M BIS-TRIS PH=5.5, 25% PEG3350, 0.20 M NH4AC, pH 5.50
Crystal Properties Matthews coefficient Solvent content 2 38.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.725 α = 90 b = 58.056 β = 90 c = 58.987 γ = 90
Symmetry Space Group P 21 21 2
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 MARRESEARCH 2005-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.8 41.49 98.3 0.14 13.95 12.79 37336
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 1.8 1.9 88.9 0.57 2.27 4.19
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W0I 1.8 50 35421 1868 98.3 0.181 0.177 0.1845 0.24 0.2415 RANDOM 16.11
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] -2.04 0.73 1.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.068 r_dihedral_angle_3_deg 14.775 r_dihedral_angle_4_deg 12.962 r_scangle_it 10.058 r_scbond_it 8.077 r_dihedral_angle_1_deg 6.444 r_mcangle_it 5.002 r_mcbond_it 3.952 r_angle_refined_deg 1.461 r_angle_other_deg 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.068 r_dihedral_angle_3_deg 14.775 r_dihedral_angle_4_deg 12.962 r_scangle_it 10.058 r_scbond_it 8.077 r_dihedral_angle_1_deg 6.444 r_mcangle_it 5.002 r_mcbond_it 3.952 r_angle_refined_deg 1.461 r_angle_other_deg 0.97 r_symmetry_vdw_other 0.231 r_symmetry_vdw_refined 0.225 r_symmetry_hbond_refined 0.208 r_nbd_refined 0.205 r_nbd_other 0.202 r_xyhbond_nbd_refined 0.189 r_nbtor_refined 0.177 r_nbtor_other 0.09 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3107 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing