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Structure of native L-amino acid oxidase from Vipera ammodytes ammodytes: stabilization of the quaternary structure by divalent ions and structural changes in the dynamic active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8R PDB entry 1F8R
Crystallization Crystal Properties Matthews coefficient Solvent content 2.32 47.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 196.978 α = 90 b = 95.839 β = 92.53 c = 108.442 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 MAR CCD 165 mm mirrors 2008-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8 EMBL/DESY, HAMBURG X13
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 2.57 27.4 97.1 0.172 10.6 7.1 63563 62717 1 1 19.3
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) 2.57 2.66 74.7 0.448 3.9 4853
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 1F8R 2.57 27.4 60346 3212 98.04 0.19537 0.19105 0.1918 0.27609 0.2731 RANDOM 19.805
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] 1 0.11 -0.74 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.41 r_dihedral_angle_4_deg 20.408 r_dihedral_angle_3_deg 20.38 r_dihedral_angle_1_deg 7.474 r_scangle_it 2.395 r_angle_refined_deg 1.523 r_scbond_it 1.467 r_mcangle_it 1.018 r_mcbond_it 0.573 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.41 r_dihedral_angle_4_deg 20.408 r_dihedral_angle_3_deg 20.38 r_dihedral_angle_1_deg 7.474 r_scangle_it 2.395 r_angle_refined_deg 1.523 r_scbond_it 1.467 r_mcangle_it 1.018 r_mcbond_it 0.573 r_nbtor_refined 0.319 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.19 r_symmetry_vdw_refined 0.173 r_metal_ion_refined 0.164 r_symmetry_hbond_refined 0.138 r_chiral_restr 0.111 r_bond_refined_d 0.012 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15456 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 272
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling