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Crystal structure of L-lactate oxidase with pyruvate complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DU2 PDB ENTRY 2DU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.24 45.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.841 α = 90 b = 118.566 β = 121.07 c = 107.237 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 QUANTUM 4 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.9 50 99.5 0.053 113367
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 2DU2 1.9 37.4 107689 5676 99.17 0.17903 0.17646 0.1763 0.22682 0.2261 RANDOM 25.131
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.505 r_dihedral_angle_3_deg 15.953 r_dihedral_angle_4_deg 14.366 r_dihedral_angle_1_deg 6.433 r_scangle_it 3.634 r_scbond_it 2.384 r_angle_refined_deg 1.661 r_mcangle_it 1.379 r_mcbond_it 0.902 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.505 r_dihedral_angle_3_deg 15.953 r_dihedral_angle_4_deg 14.366 r_dihedral_angle_1_deg 6.433 r_scangle_it 3.634 r_scbond_it 2.384 r_angle_refined_deg 1.661 r_mcangle_it 1.379 r_mcbond_it 0.902 r_nbtor_refined 0.307 r_nbd_refined 0.221 r_symmetry_vdw_refined 0.213 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.128 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11118 Nucleic Acid Atoms Solvent Atoms 1311 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction SCALEPACK data scaling CNS phasing