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Crystal Structure of Single-chain L-Glutamate Oxidase Mutant from Streptomyces sp. X-119-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E1M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293.15 0.1 M sodium acetate trihydrate (pH 4.5), 10% PEG3000 and 0.05 M zinc acetate dihydrate
Crystal Properties Matthews coefficient Solvent content 2.96 58.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 158.4 α = 90 b = 158.4 β = 90 c = 138.235 γ = 90
Symmetry Space Group I 4 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 S 6M 2020-11-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.66 49.32 100 0.999 20 13 25525
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.66 2.79 0.818
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.66 49.32 24275 1188 100 0.259 0.2082 0.305 0.2626 26
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] 15 15 -29.99
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.121 r_long_range_B_other 11.094 r_scangle_other 8.01 r_mcangle_it 7.197 r_mcangle_other 7.196 r_scbond_it 5.298 r_scbond_other 5.292 r_mcbond_it 5.003 r_mcbond_other 5 r_nbtor_refined
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 11.121 r_long_range_B_other 11.094 r_scangle_other 8.01 r_mcangle_it 7.197 r_mcangle_other 7.196 r_scbond_it 5.298 r_scbond_other 5.292 r_mcbond_it 5.003 r_mcbond_other 5 r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4691 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing