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Crystal structure of the Patched-1 (PTCH1) ectodomain 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6RTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1 M bicine/Trizma base pH 8.5,
0.03M of each ethylene glycol (diethyleneglycol, triethyleneglycol, tetraethyleneglycol and pentaethyleneglycol),
12.5% (v/v) MPD,
12.5% (w/v) PEG 1000,
12.5% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.37 48.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.17 α = 90 b = 65.68 β = 90 c = 100.28 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 2016-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97950 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 50.14 100 0.129 0.055 0.998 10.7 6.4 24282
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 1.99 99.1 0.525 0.316 1.4 5.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6RTY 1.95 50.14 23043 1185 99.89 0.19929 0.19634 0.2046 0.25696 0.2539 RANDOM 36.903
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] 2.35 -0.62 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.904 r_dihedral_angle_4_deg 20.576 r_dihedral_angle_3_deg 14.148 r_long_range_B_refined 8.533 r_long_range_B_other 8.5 r_dihedral_angle_1_deg 6.446 r_scangle_other 6.341 r_mcangle_it 3.98 r_mcangle_other 3.979 r_scbond_it 3.939
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.904 r_dihedral_angle_4_deg 20.576 r_dihedral_angle_3_deg 14.148 r_long_range_B_refined 8.533 r_long_range_B_other 8.5 r_dihedral_angle_1_deg 6.446 r_scangle_other 6.341 r_mcangle_it 3.98 r_mcangle_other 3.979 r_scbond_it 3.939 r_scbond_other 3.937 r_mcbond_it 2.711 r_mcbond_other 2.682 r_angle_refined_deg 1.429 r_angle_other_deg 1.327 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2147 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing