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Clathrin heavy chain N-terminal domain bound to a clathrin-box motif from hepatitis D virus large antigen (clade 2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 200 nL protein:peptide (20 mg/mL NTD and 3.6 mM peptide) plus 400 nL reservoir equilibrated against a 80 uL reservoir of 1.75 M sodium malonate pH 7.0
Crystal Properties Matthews coefficient Solvent content 3.64 66.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.9 α = 90 b = 131.23 β = 115.86 c = 78.45 γ = 90
Symmetry Space Group C 1 2 1
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-F KB mirrors 2013-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.96 39.2 94.6 0.081 0.996 7.2 2.5 79976
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 2 95.9 0.581 0.563 1.5 2.3
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 1C9I 1.96 39.2 79976 4224 94.42 0.17037 0.16914 0.1771 0.19343 0.2027 RANDOM 33.338
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] 0.01 -0.51 0.21 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.263 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_3_deg 14.112 r_long_range_B_refined 8.246 r_long_range_B_other 8.245 r_dihedral_angle_1_deg 7.233 r_scangle_other 3.907 r_mcangle_it 2.805 r_mcangle_other 2.805 r_scbond_it 2.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.263 r_dihedral_angle_4_deg 14.392 r_dihedral_angle_3_deg 14.112 r_long_range_B_refined 8.246 r_long_range_B_other 8.245 r_dihedral_angle_1_deg 7.233 r_scangle_other 3.907 r_mcangle_it 2.805 r_mcangle_other 2.805 r_scbond_it 2.494 r_scbond_other 2.494 r_angle_refined_deg 1.917 r_mcbond_it 1.767 r_mcbond_other 1.767 r_angle_other_deg 1.096 r_chiral_restr 0.12 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 5862 Nucleic Acid Atoms Solvent Atoms 583 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling REFMAC phasing