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Crystal structure of Hedgehog-interacting protein (HHIP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HO4 PDB entry 3HO4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 292 0.1 M sodium acetate, 0.2 M ammonium sulfate, 22-24% PEG 4000 and 1-2% dioxane, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.97 58.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.23 α = 90 b = 118.011 β = 90 c = 126.348 γ = 90
Symmetry Space Group C 2 2 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 315 vertically collimating premirror, LN2 cooled double-crystal silicon (111) monochromator, toroidal focusing M2 mirror 2006-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0000 ALS 5.0.2
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 2.8 30 99.8 0.089 14.4 4.7 14785 14755 -3
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 2.8 2.9 100 0.491 3.5 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 3HO4 2.9 30 -3 13892 13746 722 98.95 0.24229 0.24229 0.23968 0.2318 0.29153 0.2824 RANDOM 94.581
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] -7.28 -2.01 9.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.225 r_dihedral_angle_3_deg 20.23 r_dihedral_angle_4_deg 13.304 r_dihedral_angle_1_deg 5.911 r_mcangle_it 3.058 r_scangle_it 2.504 r_mcbond_it 1.795 r_scbond_it 1.522 r_angle_refined_deg 1.12 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.225 r_dihedral_angle_3_deg 20.23 r_dihedral_angle_4_deg 13.304 r_dihedral_angle_1_deg 5.911 r_mcangle_it 3.058 r_scangle_it 2.504 r_mcbond_it 1.795 r_scbond_it 1.522 r_angle_refined_deg 1.12 r_nbtor_refined 0.305 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.157 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.075 r_symmetry_hbond_refined 0.047 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3451 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose BOS data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling