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Crystal structure of Candida antarctica Lipase B with active Ser105 modified with a phosphonate inhibitor
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 1.2 M Ammonium dihydrogen phosphate, Tris
Crystal Properties Matthews coefficient Solvent content 3.22 61.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.462 α = 90 b = 123.222 β = 96.2 c = 150.316 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 ADSC QUANTUM 270 2013-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.00 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.9 50 99.7 0.108 0.108 16.3 3.7 74402
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 2.9 2.95 99.5 0.432 4.1 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.89 30.63 70652 3750 99.23 0.17407 0.17118 0.1822 0.22864 0.2365 RANDOM 36.049
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] -2.5 -1.64 4.95 -2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.798 r_dihedral_angle_4_deg 18.123 r_dihedral_angle_3_deg 16.337 r_dihedral_angle_1_deg 6.671 r_long_range_B_refined 6.068 r_long_range_B_other 6.068 r_scangle_other 3.86 r_mcangle_it 3.301 r_mcangle_other 3.301 r_scbond_it 2.348
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.798 r_dihedral_angle_4_deg 18.123 r_dihedral_angle_3_deg 16.337 r_dihedral_angle_1_deg 6.671 r_long_range_B_refined 6.068 r_long_range_B_other 6.068 r_scangle_other 3.86 r_mcangle_it 3.301 r_mcangle_other 3.301 r_scbond_it 2.348 r_scbond_other 2.348 r_mcbond_it 2.027 r_mcbond_other 2.024 r_angle_refined_deg 1.743 r_angle_other_deg 0.999 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 18514 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 432
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing