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Alditol Oxidase from Streptomyces coelicolor A3(2): Complex with Sorbitol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VFR PDB ENTRY 2VFR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 pH 6.5
Crystal Properties Matthews coefficient Solvent content 2 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.185 α = 90 b = 66.622 β = 95.09 c = 59.134 γ = 90
Symmetry Space Group C 1 2 1
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 2007-04-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.6 37.9 99.9 0.05 21.5 4.8 54653
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 1.6 1.7 100 0.24 5.2 4.8
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 2VFR 1.6 33.31 51942 2710 99.9 0.154 0.152 0.1512 0.179 0.1795 RANDOM 16.54
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] 0.16 0.11 0.91 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.56 r_dihedral_angle_4_deg 18.291 r_dihedral_angle_3_deg 11.893 r_dihedral_angle_1_deg 6.074 r_scangle_it 3.919 r_scbond_it 2.5 r_mcangle_it 1.674 r_angle_refined_deg 1.65 r_mcbond_it 1.129 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.56 r_dihedral_angle_4_deg 18.291 r_dihedral_angle_3_deg 11.893 r_dihedral_angle_1_deg 6.074 r_scangle_it 3.919 r_scbond_it 2.5 r_mcangle_it 1.674 r_angle_refined_deg 1.65 r_mcbond_it 1.129 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.276 r_symmetry_hbond_refined 0.263 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.125 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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 3111 Nucleic Acid Atoms Solvent Atoms 560 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CCP4 phasing