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Improved variant of (R)-selective manganese-dependent hydroxynitrile lyase from bacteria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BIF PDB ENTRY 4BIF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M SODIUM THIOCYANATE, 20% W/V PEG 3350 9-18 MG/ML PROTEIN CONCENTRATION (IN 20 MM TRIS/HCL PH 7.0, 200 MM NACL)
Crystal Properties Matthews coefficient Solvent content 3 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.806 α = 90 b = 93.174 β = 111.93 c = 146.671 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 287 PIXEL DECTRIS PILATUS 2014-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.1 58.3 99.5 0.09 12.2 4.3 178792 1.92
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 2.1 2.22 98.1 0.76 1.92 4.3
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 4BIF 2.1 58.28 169826 8940 99.56 0.1835 0.18082 0.1865 0.23397 0.234 RANDOM 39.479
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] -0.09 1.28 -2.87 1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.06 r_dihedral_angle_3_deg 15.682 r_dihedral_angle_4_deg 14.82 r_dihedral_angle_1_deg 6.709 r_mcangle_it 3.393 r_scbond_it 3.02 r_mcbond_it 2.39 r_mcbond_other 2.39 r_angle_refined_deg 1.464 r_angle_other_deg 0.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.06 r_dihedral_angle_3_deg 15.682 r_dihedral_angle_4_deg 14.82 r_dihedral_angle_1_deg 6.709 r_mcangle_it 3.393 r_scbond_it 3.02 r_mcbond_it 2.39 r_mcbond_other 2.39 r_angle_refined_deg 1.464 r_angle_other_deg 0.746 r_chiral_restr 0.082 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20260 Nucleic Acid Atoms Solvent Atoms 1666 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing