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Clathrin terminal domain complexed with TLPWDLWTT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C9I PDB ENTRY 1C9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 VAPOUR DIFFUSION OVER A RESERVOIR CONTAINING 20% PEG8000, 200 MM MGCL2, 4 MM DTT,100 MM CAPS PH 9, DRIED UP DROP
Crystal Properties Matthews coefficient Solvent content 2.38 48.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.301 α = 90 b = 61.301 β = 90 c = 420.52 γ = 90
Symmetry Space Group P 41 21 2
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 CCD MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
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 2.3 24.92 99.4 0.057 9.3131 5.84 37228
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 2.3 2.42 97.4 0.33 2.02 4.33
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 1C9I 2.3 105.41 35214 1856 99.2 0.197 0.194 0.2012 0.253 0.2579 RANDOM 21.21
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] 0.72 0.72 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.882 r_dihedral_angle_4_deg 21.587 r_dihedral_angle_3_deg 16.685 r_dihedral_angle_1_deg 7.194 r_scangle_it 2.912 r_scbond_it 2.065 r_angle_refined_deg 1.567 r_mcangle_it 1.506 r_mcbond_it 1.312 r_angle_other_deg 0.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.882 r_dihedral_angle_4_deg 21.587 r_dihedral_angle_3_deg 16.685 r_dihedral_angle_1_deg 7.194 r_scangle_it 2.912 r_scbond_it 2.065 r_angle_refined_deg 1.567 r_mcangle_it 1.506 r_mcbond_it 1.312 r_angle_other_deg 0.882 r_symmetry_hbond_refined 0.224 r_xyhbond_nbd_refined 0.215 r_symmetry_vdw_other 0.201 r_nbd_other 0.187 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.173 r_mcbond_other 0.172 r_chiral_restr 0.099 r_nbtor_other 0.086 r_xyhbond_nbd_other 0.039 r_bond_refined_d 0.016 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5649 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing