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Crystal structure of hexagonal form of lipase B from Candida antarctica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W9B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 294.15 24% polyethylene glycol 3350, 0.1M citric acid, and 0.1M sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.38 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.034 α = 90 b = 89.034 β = 90 c = 137.257 γ = 120
Symmetry Space Group P 63 2 2
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 OXFORD TITAN CCD 2015-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 77.11 98.1 24.58 8.8 22034
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 3W9B 2 77.11 20971 1032 98.08 0.14654 0.14413 0.1573 0.19276 0.2044 RANDOM 22.891
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] 0.32 0.16 0.32 -1.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_4_deg 17.036 r_dihedral_angle_3_deg 13.024 r_dihedral_angle_1_deg 6.744 r_long_range_B_refined 5.51 r_long_range_B_other 5.509 r_scangle_other 2.132 r_angle_refined_deg 1.964 r_mcangle_other 1.541 r_mcangle_it 1.537
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.756 r_dihedral_angle_4_deg 17.036 r_dihedral_angle_3_deg 13.024 r_dihedral_angle_1_deg 6.744 r_long_range_B_refined 5.51 r_long_range_B_other 5.509 r_scangle_other 2.132 r_angle_refined_deg 1.964 r_mcangle_other 1.541 r_mcangle_it 1.537 r_scbond_it 1.395 r_scbond_other 1.395 r_angle_other_deg 1.136 r_mcbond_it 1 r_mcbond_other 0.99 r_chiral_restr 0.119 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2324 Nucleic Acid Atoms Solvent Atoms 332 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement CrysalisPro data reduction Aimless data scaling PHASER phasing