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S221M V223F Y359A mutant of 4-Hydroxymandelate synthase from Streptomyces coelicolor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R5V PDB ENTRY 2R5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 1 MICROLITRE 10 MG ML-1 HMS VARIANT, PREINCUBATED WITH 1.25 MM COCL2 AND 2.5 MM R-MANDELATE) PLUS 1 MICROLITRE MOTHER LIQUOR. THE BEST CRYSTALS WERE ROUTINELY OBTAINED IN CRYSTAL DROPS CONTAINING 0.05 M TRIS/CL PH 9.0, 0.1 M MGCL2, 7.5% (W/V) PEG 4K AND 2.5% (V/V) 2-METHYL-1,4-PENTANEDIOL.
Crystal Properties Matthews coefficient Solvent content 2.54 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.87 α = 90 b = 122.87 β = 90 c = 54.86 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD 2012-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.95 61.44 100 0.06 15.6 6.7 57014 2
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 1.95 2.01 100 0.49 3.9 6.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2R5V 1.95 54.95 57014 3049 99.97 0.17711 0.17505 0.21504 0.2171 RANDOM 34.805
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] -0.68 -0.68 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.114 r_dihedral_angle_4_deg 18.129 r_dihedral_angle_3_deg 14.576 r_dihedral_angle_1_deg 6.715 r_mcangle_it 4.683 r_scbond_it 4.594 r_mcbond_it 3.494 r_angle_refined_deg 2.002 r_chiral_restr 0.156 r_bond_refined_d 0.021
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.114 r_dihedral_angle_4_deg 18.129 r_dihedral_angle_3_deg 14.576 r_dihedral_angle_1_deg 6.715 r_mcangle_it 4.683 r_scbond_it 4.594 r_mcbond_it 3.494 r_angle_refined_deg 2.002 r_chiral_restr 0.156 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_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 5051 Nucleic Acid Atoms Solvent Atoms 531 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing