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NHERF3 PDZ2 in Complex with a Phage-Derived Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.6 292 30% PEG 4000, 0.1 M sodium acetate (pH 4.6), 0.1 M magnesium chloride, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 153.31 α = 90 b = 153.31 β = 90 c = 34.635 γ = 120
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 MAR scanner 345 mm plate 2006-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54
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 2.05 20 94.9 0.043 37.1 5.3 18068
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 2.05 2.12 73.6 0.296 4.4 4.6 1416
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 1g9o 2.05 20 18067 939 94.91 0.1916 0.1884 0.1871 0.2516 0.2522 RANDOM 55.336
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] -2.62 -1.31 -2.62 3.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.98 r_dihedral_angle_4_deg 22.663 r_dihedral_angle_3_deg 14.459 r_dihedral_angle_1_deg 6.823 r_scangle_it 5.131 r_mcangle_it 4.202 r_scbond_it 3.825 r_mcbond_it 3.499 r_angle_refined_deg 1.476 r_angle_other_deg 0.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.98 r_dihedral_angle_4_deg 22.663 r_dihedral_angle_3_deg 14.459 r_dihedral_angle_1_deg 6.823 r_scangle_it 5.131 r_mcangle_it 4.202 r_scbond_it 3.825 r_mcbond_it 3.499 r_angle_refined_deg 1.476 r_angle_other_deg 0.921 r_mcbond_other 0.755 r_symmetry_hbond_refined 0.226 r_symmetry_vdw_other 0.218 r_symmetry_vdw_refined 0.201 r_nbd_refined 0.196 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.179 r_nbtor_refined 0.166 r_chiral_restr 0.084 r_nbtor_other 0.083 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2041 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 12
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHASER phasing