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The structure of L-amino acid oxidase from Rhodococcus opacus in complex with o-aminobenzoate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JAE PDB ENTRY 2JAE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.8 100MM HEPES PH 7.8 10% 2-PROPANOLE 10% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.4 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.649 α = 90 b = 109.676 β = 90 c = 134.368 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 IMAGE PLATE MARRESEARCH 2004-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 1.85 30 99.2 0.15 9.5 4 83174
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 1.85 1.92 98.7 0.5 2 3.8
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 2JAE 1.85 19.77 78881 4145 99.2 0.154 0.151 0.1559 0.214 0.2166 RANDOM 15.16
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] -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.674 r_dihedral_angle_4_deg 16.835 r_dihedral_angle_3_deg 12.529 r_dihedral_angle_1_deg 5.827 r_scangle_it 4.044 r_scbond_it 3.033 r_mcangle_it 1.837 r_mcbond_it 1.44 r_angle_other_deg 1.385 r_angle_refined_deg 1.341
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.674 r_dihedral_angle_4_deg 16.835 r_dihedral_angle_3_deg 12.529 r_dihedral_angle_1_deg 5.827 r_scangle_it 4.044 r_scbond_it 3.033 r_mcangle_it 1.837 r_mcbond_it 1.44 r_angle_other_deg 1.385 r_angle_refined_deg 1.341 r_gen_planes_other 0.219 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.196 r_nbd_other 0.184 r_nbtor_refined 0.184 r_symmetry_hbond_refined 0.184 r_symmetry_vdw_other 0.179 r_xyhbond_nbd_refined 0.175 r_nbtor_other 0.086 r_chiral_restr 0.084 r_gen_planes_refined 0.051 r_bond_refined_d 0.013 r_bond_other_d 0.002 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 7395 Nucleic Acid Atoms Solvent Atoms 985 Heterogen Atoms 126
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing