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Alditol Oxidase from Streptomyces coelicolor A3(2): Complex with Sulphite
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 1.99 37.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.561 α = 90 b = 68.455 β = 95.19 c = 57.965 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 2007-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.7 19.9 98.5 0.04 24.9 3.1 43108
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 1.7 1.8 97.1 0.09 10.9 3
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 1.72 19.51 40994 2108 98.6 0.153 0.152 0.1504 0.184 0.183 RANDOM 10.08
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] 0.03 -0.15 -0.07 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.663 r_dihedral_angle_4_deg 20.256 r_dihedral_angle_3_deg 10.988 r_dihedral_angle_1_deg 6.131 r_scangle_it 3.062 r_scbond_it 1.973 r_angle_refined_deg 1.73 r_mcangle_it 1.131 r_mcbond_it 0.768 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.663 r_dihedral_angle_4_deg 20.256 r_dihedral_angle_3_deg 10.988 r_dihedral_angle_1_deg 6.131 r_scangle_it 3.062 r_scbond_it 1.973 r_angle_refined_deg 1.73 r_mcangle_it 1.131 r_mcbond_it 0.768 r_nbtor_refined 0.305 r_nbd_refined 0.215 r_chiral_restr 0.203 r_xyhbond_nbd_refined 0.106 r_symmetry_hbond_refined 0.106 r_symmetry_vdw_refined 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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 3136 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling CCP4 phasing