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Crystal structure of Sonic hedgehog in complex with antibody 5E1 without metals
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 200mM KNO3, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.59 52.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.37 α = 90 b = 83.99 β = 90 c = 126.85 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 S 6M 2018-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.75 53.5 99.9 0.117 0.04 0.997 11.8 9.3 75399
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 1.75 1.84 99.7 0.943 0.339 0.693 2.3 8.5
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 (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 1.75 50.67 72234 3093 99.88 0.17677 0.17546 0.1842 0.20745 0.2158 RANDOM 25.3
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] -0.37 0.83 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.019 r_dihedral_angle_4_deg 14.228 r_dihedral_angle_3_deg 13.867 r_dihedral_angle_1_deg 7.764 r_long_range_B_refined 5.269 r_long_range_B_other 5.269 r_scangle_other 2.721 r_mcangle_it 1.84 r_mcangle_other 1.839 r_angle_refined_deg 1.825
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.019 r_dihedral_angle_4_deg 14.228 r_dihedral_angle_3_deg 13.867 r_dihedral_angle_1_deg 7.764 r_long_range_B_refined 5.269 r_long_range_B_other 5.269 r_scangle_other 2.721 r_mcangle_it 1.84 r_mcangle_other 1.839 r_angle_refined_deg 1.825 r_scbond_it 1.699 r_scbond_other 1.697 r_angle_other_deg 1.457 r_mcbond_it 1.162 r_mcbond_other 1.162 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 4467 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing