☰ Navigation Tabs
The Structure of ERBIN PDZ domain bound to the Carboxy-terminal tail of the ErbB2 Receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MFG PDB ENTRY 1MFG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 292 23-26% PEG 4000, 20% GLYCEROL, 100mM AMMONIUM ACETATE, 100mM SODIUM ACETATE, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.03 39.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.526 α = 90 b = 56.995 β = 99.16 c = 30.951 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 100 IMAGE PLATE RIGAKU RAXIS IV MIRRORS 2002-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.88 30.6 95 0.028 0.028 44.7 3.73 7196 7068 -3 13
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.88 1.95 90.2 0.096 0.096 13.3 3.34 660
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1MFG 1.88 30.57 7068 6738 330 95 0.169 0.169 0.1668 0.1806 0.2159 0.2347 RANDOM 18.168
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] -0.93 -0.24 0.35 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.462 r_scangle_it 5.323 r_scbond_it 3.033 r_mcangle_it 1.828 r_angle_refined_deg 1.579 r_mcbond_it 0.977 r_angle_other_deg 0.83 r_symmetry_vdw_other 0.346 r_nbd_other 0.258 r_nbd_refined 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.462 r_scangle_it 5.323 r_scbond_it 3.033 r_mcangle_it 1.828 r_angle_refined_deg 1.579 r_mcbond_it 0.977 r_angle_other_deg 0.83 r_symmetry_vdw_other 0.346 r_nbd_other 0.258 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.184 r_symmetry_hbond_refined 0.171 r_symmetry_vdw_refined 0.161 r_chiral_restr 0.088 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 767 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement