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Structure of L-lysine oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KVE PDB entry 3KVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293 2% (w/v) PEG 400, 0.1M HEPES pH7.6, 1.8M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 49.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.975 α = 90 b = 170.012 β = 132.01 c = 81.046 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 RAYONIX MX225HE 2012-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000 SPring-8 BL41XU
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 34.4 99.9 0.106 8.1 3 92177 92177 16.2
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 1.9 2 100 0.362 3.4 3 13448
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 PDB entry 3KVE 1.9 32.023 1.4 92171 4613 99.96 0.1603 0.1588 0.1564 0.1882 0.1852 RANDOM
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] -0.6639 -0.4098 -0.2063 0.8702
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.048 f_angle_d 1.243 f_chiral_restr 0.104 f_bond_d 0.007 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8086 Nucleic Acid Atoms Solvent Atoms 786 Heterogen Atoms 166
Software Software Software Name Purpose SPring-8 data collection PHENIX model building PHENIX refinement MOSFLM data reduction SCALA data scaling PHENIX phasing