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Crystal structure of wild-type SCP2 thiolase from Leishmania mexicana at 1.85 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AFW PDB ENTRY 1AFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 100 MM MES PH6.5, 10% MME PEG5000, 10% DMSO, 10% MPD
Crystal Properties Matthews coefficient Solvent content 3.05 59.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.249 α = 90 b = 122.249 β = 90 c = 133.081 γ = 120
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 MARMOSAIC 225 mm CCD MIRRORS 2011-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.85 31.74 100 0.12 11.9 10.7 95952
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 1.85 1.95 100 0.93 2.3 10.2
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 1AFW 1.85 105.87 91098 4797 99.98 0.16363 0.16195 0.19557 0.1938 RANDOM 22.865
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] 1.28 0.64 1.28 -1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.55 r_dihedral_angle_4_deg 17.068 r_dihedral_angle_3_deg 13.411 r_dihedral_angle_1_deg 6.308 r_angle_refined_deg 1.809 r_angle_other_deg 1.251 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.55 r_dihedral_angle_4_deg 17.068 r_dihedral_angle_3_deg 13.411 r_dihedral_angle_1_deg 6.308 r_angle_refined_deg 1.809 r_angle_other_deg 1.251 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.005 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 6466 Nucleic Acid Atoms Solvent Atoms 569 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing