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Crystal structure of Staphylococcus hyicus lipase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JI3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 NaCl, Na succinate, DMSO, isopropanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.51 50.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.31 α = 90 b = 77.96 β = 90 c = 169.81 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 277 IMAGE PLATE MARRESEARCH 1994-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X31 1.0 EMBL/DESY, HAMBURG X31
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.86 26.71 99 0.088 6.1 22929 22929
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.86 2.93 99.7 1663
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1JI3 2.86 26.71 22929 22929 2322 100 0.213 0.213 0.208 0.217 0.263 0.2676 RANDOM 18.51
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] 0.04 -0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.146 r_dihedral_angle_3_deg 19.114 r_dihedral_angle_4_deg 18.157 r_dihedral_angle_1_deg 4.783 r_angle_refined_deg 0.786 r_angle_other_deg 0.584 r_scangle_it 0.582 r_scbond_it 0.355 r_mcangle_it 0.286 r_symmetry_vdw_other 0.231
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.146 r_dihedral_angle_3_deg 19.114 r_dihedral_angle_4_deg 18.157 r_dihedral_angle_1_deg 4.783 r_angle_refined_deg 0.786 r_angle_other_deg 0.584 r_scangle_it 0.582 r_scbond_it 0.355 r_mcangle_it 0.286 r_symmetry_vdw_other 0.231 r_xyhbond_nbd_refined 0.216 r_nbd_refined 0.202 r_nbd_other 0.192 r_nbtor_refined 0.19 r_symmetry_vdw_refined 0.172 r_mcbond_it 0.164 r_metal_ion_refined 0.13 r_symmetry_hbond_refined 0.126 r_nbtor_other 0.088 r_chiral_restr 0.049 r_mcbond_other 0.03 r_bond_refined_d 0.005 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6143 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 4
Software Software Software Name Purpose AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling