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Crystal structure of multi-copper oxidase from Pediococcus acidilactici
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 52.5 nL drop composed of 95 mM Sodium Citrate buffer, pH 3.0, 3% polyethylene glycol 8000, 7.8% polyethylene glycol 400, 1.2% dimethyl sulfoxide, 114 mM benzamidine hydrochloride, and 5.0-10.0 mg/mL protein in 5 mM Tris-HCL pH 7.2
Mylar was initially used as the surface, resulting in thin polycrystalline needles. Changing the surface to COC (cyclic olefin copolymer) resulted in large high-quality single crystals.
Crystal Properties Matthews coefficient Solvent content 2.47 50.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.06 α = 90 b = 147.3 β = 98.55 c = 65.46 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS EIGER X 9M 2019-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9202 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.78 73.65 98.3 0.185 0.999 10.37 25.53 98773
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.82 77.6 0.4263 0.476 0.71
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.8 73.65 92098 4742 99.97 0.11624 0.1139 0.1246 0.161 0.1648 RANDOM 47.028
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] 0.44 1 -0.23 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.007 r_sphericity_free 29.463 r_sphericity_bonded 18.229 r_dihedral_angle_3_deg 18.097 r_dihedral_angle_4_deg 17.055 r_scangle_other 9.509 r_scbond_it 9.229 r_scbond_other 9.229 r_long_range_B_refined 8.301 r_long_range_B_other 8.226
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.007 r_sphericity_free 29.463 r_sphericity_bonded 18.229 r_dihedral_angle_3_deg 18.097 r_dihedral_angle_4_deg 17.055 r_scangle_other 9.509 r_scbond_it 9.229 r_scbond_other 9.229 r_long_range_B_refined 8.301 r_long_range_B_other 8.226 r_dihedral_angle_1_deg 7.573 r_mcangle_other 6.614 r_mcangle_it 6.613 r_rigid_bond_restr 6.057 r_mcbond_it 5.978 r_mcbond_other 5.958 r_angle_refined_deg 2.579 r_angle_other_deg 1.275 r_chiral_restr 0.2 r_bond_refined_d 0.03 r_gen_planes_refined 0.012 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7622 Nucleic Acid Atoms Solvent Atoms 609 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing