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Structure-based redesign of cofactor binding in Putrescine Oxidase: P15I-A394C double mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YG3 PDB ENTRY 2YG3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.4 pH 6.4
Crystal Properties Matthews coefficient Solvent content 3.68 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 198.45 α = 90 b = 80.29 β = 90 c = 91.43 γ = 90
Symmetry Space Group P 21 21 2
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 210 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 2.5 30 99.5 0.1 11.2 5 51121
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 2.5 2.6 100 0.6 5.5 5
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 2YG3 2.5 51.05 48434 2578 99.25 0.18628 0.18399 0.1832 0.23081 0.2276 RANDOM 19.821
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] 0.96 0.29 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.578 r_dihedral_angle_4_deg 20.237 r_dihedral_angle_3_deg 15.984 r_dihedral_angle_1_deg 6.379 r_scangle_it 5.423 r_scbond_it 3.347 r_angle_refined_deg 1.911 r_mcangle_it 1.875 r_mcbond_it 0.927 r_chiral_restr 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.578 r_dihedral_angle_4_deg 20.237 r_dihedral_angle_3_deg 15.984 r_dihedral_angle_1_deg 6.379 r_scangle_it 5.423 r_scbond_it 3.347 r_angle_refined_deg 1.911 r_mcangle_it 1.875 r_mcbond_it 0.927 r_chiral_restr 0.12 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 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_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 6910 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CCP4 phasing