☰ Navigation Tabs
Crystal structure of a platinum-bound S445C mutant of Pseudomonas sp. MIS38 lipase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z8X PDB ENTRY 2Z8X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 20% PEG 20000, 0.1M MES, 0.2M calcium acetate, 5mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.82 56.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.879 α = 90 b = 84.404 β = 96.5 c = 87.012 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 RIGAKU JUPITER 210 mirror 2007-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.071784 SPring-8 BL38B1
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 50 0.074 7.2 65946 63435 3.4
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 2Z8X 1.8 32.12 60247 3178 99.28 0.17512 0.17353 0.1828 0.20493 0.2136 RANDOM 21.877
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.107 r_dihedral_angle_4_deg 19.323 r_dihedral_angle_3_deg 12.777 r_dihedral_angle_1_deg 8.353 r_scangle_it 3.952 r_scbond_it 2.715 r_angle_refined_deg 1.771 r_mcangle_it 1.702 r_mcbond_it 1.149 r_angle_other_deg 1.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.107 r_dihedral_angle_4_deg 19.323 r_dihedral_angle_3_deg 12.777 r_dihedral_angle_1_deg 8.353 r_scangle_it 3.952 r_scbond_it 2.715 r_angle_refined_deg 1.771 r_mcangle_it 1.702 r_mcbond_it 1.149 r_angle_other_deg 1.047 r_symmetry_metal_ion_refined 0.793 r_mcbond_other 0.346 r_nbd_refined 0.233 r_symmetry_vdw_other 0.196 r_nbd_other 0.19 r_nbtor_refined 0.183 r_chiral_restr 0.173 r_symmetry_vdw_refined 0.173 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.149 r_metal_ion_refined 0.11 r_nbtor_other 0.087 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4553 Nucleic Acid Atoms Solvent Atoms 495 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing