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Crystal structure of lipase from Rhizopus microsporus var. chinensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LGY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 295 25mM Tris pH 8.0, 150mM NaCl, 0.25M (NH4)2SO4, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 3.25 62.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.225 α = 90 b = 86.225 β = 90 c = 101.151 γ = 120
Symmetry Space Group P 31 2 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 ADSC QUANTUM 315r 2012-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0 NSRRC BL13B1
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 25 100 0.1 25.72 10.3 30238
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 2.07 0.5
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 1LGY 2 25 28451 1421 99.92 0.16959 0.1676 0.1787 0.20829 0.2086 RANDOM 38.055
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] 1.94 0.97 1.94 -6.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.332 r_dihedral_angle_4_deg 19.267 r_dihedral_angle_3_deg 16.55 r_long_range_B_refined 9.135 r_long_range_B_other 9.051 r_scangle_other 7.952 r_dihedral_angle_1_deg 7.928 r_scbond_it 6.158 r_scbond_other 6.144 r_mcangle_it 5.157
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.332 r_dihedral_angle_4_deg 19.267 r_dihedral_angle_3_deg 16.55 r_long_range_B_refined 9.135 r_long_range_B_other 9.051 r_scangle_other 7.952 r_dihedral_angle_1_deg 7.928 r_scbond_it 6.158 r_scbond_other 6.144 r_mcangle_it 5.157 r_mcangle_other 5.157 r_mcbond_it 4.198 r_mcbond_other 4.191 r_angle_refined_deg 1.505 r_angle_other_deg 0.825 r_chiral_restr 0.118 r_gen_planes_refined 0.018 r_bond_refined_d 0.011 r_gen_planes_other 0.002 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2217 Nucleic Acid Atoms Solvent Atoms 212 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing