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Biosynthetic thiolase from Z. ramigera. Complex of the C89A mutant with coenzyme A.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1M3Z PDB ENTRY 1M3Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 pH 5
Crystal Properties Matthews coefficient Solvent content 2.9 57.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.22 α = 90 b = 79.57 β = 92.1 c = 148.92 γ = 90
Symmetry Space Group P 1 21 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 MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 EMBL/DESY, HAMBURG X13
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 2.3 20 97.2 0.07 15.6 3.5 87692 -3
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 2.3 2.4 86.1 0.27 4.8 2.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1M3Z 2.3 20 80970 4262 97.37 0.22407 0.22206 0.26245 0.252 RANDOM 36.916
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] -1.4 -0.61 -1.47 2.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.456 r_dihedral_angle_4_deg 16.469 r_dihedral_angle_3_deg 14.23 r_dihedral_angle_1_deg 5.565 r_scangle_it 1.815 r_scbond_it 1.267 r_angle_refined_deg 1.127 r_mcangle_it 0.821 r_angle_other_deg 0.778 r_mcbond_it 0.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.456 r_dihedral_angle_4_deg 16.469 r_dihedral_angle_3_deg 14.23 r_dihedral_angle_1_deg 5.565 r_scangle_it 1.815 r_scbond_it 1.267 r_angle_refined_deg 1.127 r_mcangle_it 0.821 r_angle_other_deg 0.778 r_mcbond_it 0.658 r_symmetry_vdw_other 0.256 r_symmetry_vdw_refined 0.255 r_symmetry_hbond_refined 0.209 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.182 r_nbd_other 0.178 r_nbtor_refined 0.164 r_nbtor_other 0.082 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.002 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 11248 Nucleic Acid Atoms Solvent Atoms 805 Heterogen Atoms 222
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling