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Gamma-adaptin appendage domain from clathrin adaptor AP1, L762E mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GYU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.4 50MM HEPES PH7.4,0.9M NA/K TARTRATE 20% W/V GLYCEROL, pH 7.40
Crystal Properties Matthews coefficient Solvent content 2.32 47.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.72 α = 90 b = 54.82 β = 90 c = 67.48 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 IMAGE PLATE MARRESEARCH OSMIC 2000-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200
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 1.7 18.7 99.6 0.062 22 6.4 14209 6
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 1.7 1.8 97.9 0.279 6 6.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1GYU 1.71 42.64 12740 1408 99.8 0.182 0.178 0.225 0.2274 RANDOM 15.94
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] -0.25 0.09 0.16
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.158 r_scbond_it 3.113 r_mcangle_it 2.282 r_angle_other_deg 1.85 r_mcbond_it 1.327 r_dihedral_angle_3_deg 0.868 r_symmetry_hbond_refined 0.434 r_xyhbond_nbd_refined 0.393 r_nbd_refined 0.228 r_nbd_other 0.217
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 5.158 r_scbond_it 3.113 r_mcangle_it 2.282 r_angle_other_deg 1.85 r_mcbond_it 1.327 r_dihedral_angle_3_deg 0.868 r_symmetry_hbond_refined 0.434 r_xyhbond_nbd_refined 0.393 r_nbd_refined 0.228 r_nbd_other 0.217 r_symmetry_vdw_other 0.165 r_chiral_restr 0.118 r_bond_refined_d 0.021 r_symmetry_vdw_refined 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_angle_refined_deg r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 935 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling