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Crystal structure of human tyrosinase-related protein 1 (TYRP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5M8L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 PEG 6000, zinc chloride, Tris-HCl pH 8.0
Crystal Properties Matthews coefficient Solvent content 4.31 71.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.754 α = 90 b = 103.754 β = 90 c = 140.988 γ = 120
Symmetry Space Group P 32 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 PIXEL DECTRIS PILATUS3 2M 2020-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.227 50 99.06 0.1136 0.1295 0.06149 0.994 6.55 4.4 81266 44.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.24 2.29 86.53 1.158 0.6229 0.46 4.1
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.228 44.967 42682 2108 98.043 0.172 0.1698 0.2127 0.2116 RANDOM 52.36
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] 0.698 0.349 0.698 -2.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.198 r_dihedral_angle_3_deg 14.569 r_lrange_other 11.199 r_lrange_it 11.177 r_dihedral_angle_2_deg 9.925 r_scangle_it 9.837 r_scangle_other 9.835 r_mcangle_it 6.899 r_mcangle_other 6.898 r_scbond_it 6.783
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.198 r_dihedral_angle_3_deg 14.569 r_lrange_other 11.199 r_lrange_it 11.177 r_dihedral_angle_2_deg 9.925 r_scangle_it 9.837 r_scangle_other 9.835 r_mcangle_it 6.899 r_mcangle_other 6.898 r_scbond_it 6.783 r_scbond_other 6.783 r_dihedral_angle_1_deg 6.56 r_mcbond_it 4.791 r_mcbond_other 4.789 r_angle_refined_deg 1.868 r_angle_other_deg 0.662 r_symmetry_nbd_refined 0.375 r_symmetry_xyhbond_nbd_other 0.344 r_metal_ion_refined 0.287 r_nbd_other 0.219 r_nbd_refined 0.218 r_xyhbond_nbd_refined 0.218 r_symmetry_nbd_other 0.198 r_chiral_restr 0.186 r_nbtor_refined 0.182 r_symmetry_metal_ion_refined 0.118 r_symmetry_nbtor_other 0.115 r_symmetry_xyhbond_nbd_refined 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3571 Nucleic Acid Atoms Solvent Atoms 182 Heterogen Atoms 279
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing