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Crystal Structure of Hedgehog Bound to the FNIII Domains of Ihog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IBB PDB Entry 2IBB PDB Entry 1VHH experimental model PDB 1VHH PDB Entry 2IBB PDB Entry 1VHH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 2.0M Na/K phosphate pH 6.4, 0.2M lithium sulfate, 0.05M CAPS pH 10.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.47 50.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.354 α = 90 b = 70.003 β = 90.18 c = 155.695 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 4 2005-10-02 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9763 NSLS X4A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 50 100 0.123 11.6 3.8 82885
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 100 0.817 1.8 3.8
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 PDB Entry 2IBB
PDB Entry 1VHH 2.2 37.68 76254 3864 92.22 0.2 0.198 0.1997 0.246 0.2473 RANDOM 39.719
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] 2.82 0.31 -1.49 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.833 r_dihedral_angle_4_deg 17.104 r_dihedral_angle_3_deg 16.785 r_dihedral_angle_1_deg 6.844 r_scangle_it 2.56 r_scbond_it 1.669 r_angle_refined_deg 1.456 r_mcangle_it 1.104 r_mcbond_it 0.679 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.833 r_dihedral_angle_4_deg 17.104 r_dihedral_angle_3_deg 16.785 r_dihedral_angle_1_deg 6.844 r_scangle_it 2.56 r_scbond_it 1.669 r_angle_refined_deg 1.456 r_mcangle_it 1.104 r_mcbond_it 0.679 r_nbtor_refined 0.309 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.205 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.145 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11295 Nucleic Acid Atoms Solvent Atoms 289 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing