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STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Ile238Thr 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 = 129.896 α = 90 b = 129.896 β = 90 c = 133.383 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 2.55 30 98.9 0.101 2.2 33857
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 2.55 40 33857 1778 98.9 0.21 0.207 0.2074 0.272 0.2722 RANDOM 46.57
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] -1.88 -1.88 3.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.993 r_scangle_it 2.628 r_scbond_it 1.665 r_angle_refined_deg 1.523 r_mcangle_it 1.058 r_mcbond_it 0.561 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.218 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.993 r_scangle_it 2.628 r_scbond_it 1.665 r_angle_refined_deg 1.523 r_mcangle_it 1.058 r_mcbond_it 0.561 r_nbd_refined 0.224 r_symmetry_vdw_refined 0.218 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.102 r_symmetry_hbond_refined 0.056 r_bond_refined_d 0.015 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 8700 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling CCP4 phasing