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Crystal structure of human tyrosinase related protein 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NM8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295.15 0.1 M Tris (pH 7.0),
0.2 M NaCl and 30% (w/v) PEG 3000
Crystal Properties Matthews coefficient Solvent content 3.03 59.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.424 α = 90 b = 141.758 β = 90 c = 191.741 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 PILATUS 6M-F 2015-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.976 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.35 48.98 99.7 6.6 4.8 102816
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3NM8 2.35 47.466 1.34 102816 5075 99.62 0.2161 0.214 0.216 0.2549 0.2567 39.7985
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 14.433 f_angle_d 1.107 f_chiral_restr 0.066 f_bond_d 0.011 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14240 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 705
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction PHENIX phasing