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Crystal structure Sonic hedgehog bound to the 5E1 fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VHH PDB entry 1VHH, refined fab
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 292 protein solution (20 mM Hepes, pH 7.2, 0.1 M NaCl, 5 mM CaCl2) was mixed with equal volume of well solution (0.2 M lithium sulfate, 100 mM Hepes, pH 7.5, and 22% w/v PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.29 46.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.306 α = 90 b = 90.544 β = 90 c = 111.672 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 CCD ADSC QUANTUM 210 Single crystal, cylindrically bent, Si(220) 2009-01-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 0.97740 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (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 1.83 50 98.8 0.068 16.4 4.3 54683 -3 19.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.9 90.7 0.464 2.2 2.6 4917
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB entry 1VHH, refined fab 1.83 47.51 -3 54255 5441 98.86 0.18056 0.18056 0.17639 0.1768 0.21844 0.2212 RANDOM 25.797
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] -0.85 0.54 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.743 r_dihedral_angle_4_deg 15.895 r_dihedral_angle_3_deg 11.538 r_dihedral_angle_1_deg 6.486 r_scangle_it 4.446 r_mcangle_it 3.46 r_scbond_it 3.063 r_mcbond_it 2.596 r_angle_refined_deg 1.255 r_symmetry_hbond_refined 0.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.743 r_dihedral_angle_4_deg 15.895 r_dihedral_angle_3_deg 11.538 r_dihedral_angle_1_deg 6.486 r_scangle_it 4.446 r_mcangle_it 3.46 r_scbond_it 3.063 r_mcbond_it 2.596 r_angle_refined_deg 1.255 r_symmetry_hbond_refined 0.362 r_nbtor_refined 0.3 r_nbd_refined 0.196 r_symmetry_vdw_refined 0.183 r_metal_ion_refined 0.15 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.088 r_bond_refined_d 0.011 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4537 Nucleic Acid Atoms Solvent Atoms 423 Heterogen Atoms 18
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling