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Crystal structure of carbohydrate oxidase from Microdochium nivale in complex with substrate analogue
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 3.1 60.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.04 α = 90 b = 56.92 β = 95.55 c = 86.9 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 120 CCD Oxford Diffraction Atlas CCD Enhance Ultra 2008-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA
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 2.1 15 90.1 0.047 15.5 2.2 33917 33917 -100 26.7
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 2.1 2.21 63.1 0.171 3.6 1.3 4312
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 2.1 15 33917 33917 90.11 0.145 0.142 18
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] 0.25 -1.4 -0.54 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.791 r_dihedral_angle_4_deg 19.708 r_dihedral_angle_3_deg 12.754 r_dihedral_angle_1_deg 6.698 r_angle_refined_deg 1.437 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.791 r_dihedral_angle_4_deg 19.708 r_dihedral_angle_3_deg 12.754 r_dihedral_angle_1_deg 6.698 r_angle_refined_deg 1.437 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 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 3714 Nucleic Acid Atoms Solvent Atoms 613 Heterogen Atoms 133
Software Software Software Name Purpose CrysalisPro data collection MOLREP phasing REFMAC refinement CrysalisPro data reduction Jana2006 data scaling