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Crystal structure of carbohydrate oxidase from Microdochium nivale
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZR6 PDB ENTRY 1ZR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 0.01 M zinc sulfate, 0.1 M MES, 12% PEG550 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.15 60.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.71 α = 90 b = 56.96 β = 95.85 c = 87.05 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 IMAGE PLATE MAR555 FLAT PANEL elliptically bent 12 quartz segments 2007-11-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.4 15 95.5 0.098 11.7 2.9 24502 24502 -3 32.5
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 2.4 2.55 95.2 0.362 3.42 2.8 3807
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 1ZR6 2.4 15 24502 24502 95.5 0.156 0.155 14.9
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] -0.13 -1.52 -0.13 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.586 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 14.857 r_dihedral_angle_1_deg 6.466 r_angle_refined_deg 1.32 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.586 r_dihedral_angle_4_deg 17.5 r_dihedral_angle_3_deg 14.857 r_dihedral_angle_1_deg 6.466 r_angle_refined_deg 1.32 r_chiral_restr 0.093 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3713 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 93
Software Software Software Name Purpose MOLREP phasing REFMAC refinement d*TREK data reduction d*TREK data scaling