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SITE DIRECTED MUTAGENESIS OF KEY RESIDUES INVOLVED IN THE CATALYTIC MECHANISM OF CYANASE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DW9 PDB ENTRY 1DW9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY THE SITTING DROP METHOD OF VAPOUR DIFFUSION FROM 50% AMMONIUM SULPHATE SOLUTIONS BUFFERED WITH 50MM NAKPO4, PH = 7.3, AND IN THE PRESENCE OF 50 MM TRIC/HCL, PH =7.3.
Crystal Properties Matthews coefficient Solvent content 1.67 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.24 α = 61.9 b = 82.6 β = 72.35 c = 84.3 γ = 69.56
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 CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 1.88 100 96.8 0.03 24 2.1 142191
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 1.88 1.95 92.8 0.14 5.1 1.9
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DW9 1.88 76.7 135079 7109 96.9 0.14 0.138 0.184 RANDOM 13.25
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] -0.34 -0.09 -0.46 -0.1 0.98 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.496 r_dihedral_angle_4_deg 12.73 r_dihedral_angle_3_deg 12.701 r_dihedral_angle_1_deg 6.429 r_scangle_it 3.732 r_scbond_it 2.841 r_angle_refined_deg 1.614 r_mcangle_it 1.316 r_mcbond_it 1.225 r_angle_other_deg 1.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.496 r_dihedral_angle_4_deg 12.73 r_dihedral_angle_3_deg 12.701 r_dihedral_angle_1_deg 6.429 r_scangle_it 3.732 r_scbond_it 2.841 r_angle_refined_deg 1.614 r_mcangle_it 1.316 r_mcbond_it 1.225 r_angle_other_deg 1.053 r_nbd_refined 0.225 r_nbd_other 0.204 r_symmetry_hbond_refined 0.199 r_symmetry_vdw_other 0.192 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.171 r_symmetry_vdw_refined 0.141 r_chiral_restr 0.108 r_nbtor_other 0.083 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other 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_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 11960 Nucleic Acid Atoms Solvent Atoms 2469 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing