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Crystal structure of D337A 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 6.5 277 10% PEG20000, 0.1M MES, 0.2M calcium acetate, 5mM zinc acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.8 56.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.601 α = 90 b = 84.324 β = 96.25 c = 86.901 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 mirrors 2007-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 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 2.25 86.39 0.062 5.2 33670 32025
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 2Z8X 2.25 39.69 30382 1627 94.91 0.17081 0.16873 0.20992 0.2089 RANDOM 19.541
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] 1.55 -1.06 -0.61 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.436 r_dihedral_angle_4_deg 18.065 r_dihedral_angle_3_deg 13.572 r_dihedral_angle_1_deg 7.07 r_scangle_it 3.374 r_scbond_it 2.32 r_mcangle_it 1.642 r_angle_refined_deg 1.573 r_mcbond_it 0.97 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.436 r_dihedral_angle_4_deg 18.065 r_dihedral_angle_3_deg 13.572 r_dihedral_angle_1_deg 7.07 r_scangle_it 3.374 r_scbond_it 2.32 r_mcangle_it 1.642 r_angle_refined_deg 1.573 r_mcbond_it 0.97 r_nbtor_refined 0.305 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.202 r_metal_ion_refined 0.111 r_symmetry_hbond_refined 0.106 r_chiral_restr 0.102 r_symmetry_metal_ion_refined 0.076 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4550 Nucleic Acid Atoms Solvent Atoms 501 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing