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Crystal structure of human tyrosinase-related protein 1 (TYRP1) in complex with (s)-amino-L-tyrosine
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, SITTING DROP 7.5 277 Sodium bromide, Bis-Tris propane, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.95 58.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.972 α = 90 b = 126.973 β = 90 c = 212.339 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 2M 2021-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.965459 ESRF MASSIF-1
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 2.198 47.26 99.51 0.0886 0.1052 0.05616 0.996 8.29 3.4 234158 40.36
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 2.2 2.22 88.35 1.377 0.9268 0.395 0.59 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 47.26 1.33 122304 6087 99.51 0.1913 0.1891 0.1878 0.2327 0.2316 43.57
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.6453 f_angle_d 1.0275 f_chiral_restr 0.0634 f_plane_restr 0.0093 f_bond_d 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14309 Nucleic Acid Atoms Solvent Atoms 999 Heterogen Atoms 1252
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing