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Crystal structure of D157A 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 2.77 55.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.634 α = 90 b = 84.627 β = 96.85 c = 87.521 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 2008-02-14 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 2.2 50 0.086 5.2 64807 33445
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 2.2 2.28 0.134 4.1
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 2.21 20 31717 1674 94.1 0.16806 0.16449 0.1811 0.23446 0.2377 RANDOM 33.382
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] -0.46 0.13 0.36 0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.518 r_dihedral_angle_4_deg 18.891 r_dihedral_angle_3_deg 16.463 r_dihedral_angle_1_deg 7.706 r_scangle_it 4.462 r_scbond_it 3.279 r_mcangle_it 2.044 r_angle_refined_deg 2.003 r_mcbond_it 1.39 r_symmetry_metal_ion_refined 0.573
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.518 r_dihedral_angle_4_deg 18.891 r_dihedral_angle_3_deg 16.463 r_dihedral_angle_1_deg 7.706 r_scangle_it 4.462 r_scbond_it 3.279 r_mcangle_it 2.044 r_angle_refined_deg 2.003 r_mcbond_it 1.39 r_symmetry_metal_ion_refined 0.573 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.272 r_symmetry_vdw_refined 0.263 r_nbd_refined 0.243 r_xyhbond_nbd_refined 0.218 r_chiral_restr 0.135 r_metal_ion_refined 0.135 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4550 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing