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Structure of Lactate Oxidase at pH4.5 from AEROCOCCUS VIRIDANS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GOX PDB ENTRY 1GOX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 40% Ethylene Glycol, 100mM acetate buffer (pH 4.5), VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties Matthews coefficient Solvent content 2.44 49.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.595 α = 90 b = 132.595 β = 90 c = 90.91 γ = 90
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 210 2005-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 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 1.81 50 99.5 0.07 61.3 14.8 71662 71313 23.9
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) 1.81 1.87 97.5 0.359 6.9 13.6 6967
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 1GOX 1.81 34.09 67698 3612 99.74 0.18557 0.18437 0.183 0.20757 0.2055 RANDOM 27.679
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.343 r_dihedral_angle_3_deg 13.109 r_dihedral_angle_4_deg 13.023 r_dihedral_angle_1_deg 5.522 r_scangle_it 3.934 r_scbond_it 2.53 r_mcangle_it 1.606 r_angle_refined_deg 1.421 r_mcbond_it 1.025 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.343 r_dihedral_angle_3_deg 13.109 r_dihedral_angle_4_deg 13.023 r_dihedral_angle_1_deg 5.522 r_scangle_it 3.934 r_scbond_it 2.53 r_mcangle_it 1.606 r_angle_refined_deg 1.421 r_mcbond_it 1.025 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.102 r_bond_refined_d 0.015 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 5228 Nucleic Acid Atoms Solvent Atoms 395 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing