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Structural and catalytic characterization of molinate hydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other inhouse structure of SeMet- mutant
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.095M sodium citrate tribasic dihydrate, pH 5.6-6.4, 19% v/v 2-propanol, 19% polyethylene glycol 4000, 5% v/v glycerol
ZnCl2
Crystal Properties Matthews coefficient Solvent content 2.58 52.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 367.696 α = 90 b = 99.079 β = 109.61 c = 131.337 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS 6M-F 2014-04-14 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2010-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 1.265 ESRF ID23-1 2 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9736, 2.13 ESRF ID14-4
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 2.27 100 93.6 12.2 2.66 183046
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 inhouse structure of SeMet- mutant 2.27 123.72 183046 9639 94.47 0.20234 0.20095 0.2075 0.22864 0.2329 RANDOM 49.423
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.986 r_dihedral_angle_4_deg 22.334 r_dihedral_angle_3_deg 16.235 r_long_range_B_refined 9.036 r_long_range_B_other 9.029 r_scangle_other 6.965 r_dihedral_angle_1_deg 6.075 r_mcangle_other 5.799 r_mcangle_it 5.798 r_scbond_it 4.596
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.986 r_dihedral_angle_4_deg 22.334 r_dihedral_angle_3_deg 16.235 r_long_range_B_refined 9.036 r_long_range_B_other 9.029 r_scangle_other 6.965 r_dihedral_angle_1_deg 6.075 r_mcangle_other 5.799 r_mcangle_it 5.798 r_scbond_it 4.596 r_scbond_other 4.596 r_mcbond_it 4.047 r_mcbond_other 4.045 r_angle_refined_deg 1.548 r_angle_other_deg 1.297 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.006 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 28776 Nucleic Acid Atoms Solvent Atoms 602 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction SHARP phasing XSCALE data scaling