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The crystal structure of lactate oxidase
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 7.5 20% PEG 4000, 10% ISOPROPANOL, 0.1M HEPES AT PH 7.5, AND 0.1M NA-L-LACTATE
Crystal Properties Matthews coefficient Solvent content 2.2 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.34 α = 90 b = 134.74 β = 90 c = 185.56 γ = 90
Symmetry Space Group P 21 21 21
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 CCD 2005-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 50 100 0.02 6.6 4.2 171468 2.4
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 2.15 100 0.05 2.4 4.2
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GOX 2.1 12 167801 2543 100 0.201 0.2 0.2035 0.257 RANDOM 13.35
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] -0.36 -1.1 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.063 r_dihedral_angle_3_deg 16.531 r_dihedral_angle_4_deg 16.077 r_dihedral_angle_1_deg 6.015 r_scangle_it 2.431 r_scbond_it 1.54 r_angle_refined_deg 1.317 r_mcangle_it 0.909 r_mcbond_it 0.535 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.063 r_dihedral_angle_3_deg 16.531 r_dihedral_angle_4_deg 16.077 r_dihedral_angle_1_deg 6.015 r_scangle_it 2.431 r_scbond_it 1.54 r_angle_refined_deg 1.317 r_mcangle_it 0.909 r_mcbond_it 0.535 r_nbtor_refined 0.303 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.18 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.144 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 22316 Nucleic Acid Atoms Solvent Atoms 1330 Heterogen Atoms 249
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing