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STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Phe454Tyr Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VAO PDB ENTRY 2VAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Crystal Properties Matthews coefficient Solvent content 2.3 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.9 α = 90 b = 129.9 β = 90 c = 133.608 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 100 IMAGE PLATE MARRESEARCH MIRRORS 2002-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 2.7 30 97.6 0.088 2.1 28185
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 2.7 2.85 94.6 0.388 3 2
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 2VAO 2.7 40 28185 1508 97.6 0.208 0.203 0.2029 0.293 0.2833 RANDOM 53.27
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] -2.35 -2.35 4.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.36 r_scangle_it 2.727 r_scbond_it 1.645 r_angle_refined_deg 1.567 r_mcangle_it 1.046 r_mcbond_it 0.547 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.225 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.36 r_scangle_it 2.727 r_scbond_it 1.645 r_angle_refined_deg 1.567 r_mcangle_it 1.046 r_mcbond_it 0.547 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.225 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 8704 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CCP4 phasing