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Tyrosinase from halophilic bacterium Hahella sp. CCB MM4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 300 0.2 M LiSO4, 0.1 Bis-Tris pH 5.5, 20 % (w/v) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.13 42.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.14 α = 90 b = 55.572 β = 90 c = 156.298 γ = 90
Symmetry Space Group P 2 2 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 PIXEL DECTRIS EIGER X 9M 2022-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
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 1.965 78.271 99.2 0.081 0.997 9.7 3.7 32382
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 1.965 1.999 100 0.565 0.781 3.7
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Alphafold 1.965 78.271 32381 1557 99.164 0.177 0.1748 0.2262 0.2372 32.633
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] 2.961 -1.926 -1.035
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.102 r_dihedral_angle_6_deg 16.539 r_dihedral_angle_2_deg 10.55 r_lrange_other 9.337 r_lrange_it 9.322 r_scangle_it 8.082 r_scangle_other 8.081 r_dihedral_angle_1_deg 8.049 r_scbond_it 6.438 r_scbond_other 6.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.102 r_dihedral_angle_6_deg 16.539 r_dihedral_angle_2_deg 10.55 r_lrange_other 9.337 r_lrange_it 9.322 r_scangle_it 8.082 r_scangle_other 8.081 r_dihedral_angle_1_deg 8.049 r_scbond_it 6.438 r_scbond_other 6.437 r_mcangle_other 5.354 r_mcangle_it 5.348 r_mcbond_other 4.136 r_mcbond_it 4.133 r_angle_refined_deg 2.111 r_angle_other_deg 0.735 r_nbd_other 0.316 r_symmetry_nbd_refined 0.241 r_nbd_refined 0.233 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.189 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.09 r_symmetry_xyhbond_nbd_refined 0.078 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3408 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing