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7th PDZ domain of Multiple PDZ Domain Protein MPDZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I92 PDB ENTRY 1I92, 1G90 experimental model PDB 1G90 PDB ENTRY 1I92, 1G90
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.2M NAF, 0.1M BISTRIS PROPANE PH8.5, 20% PEG3350, 10% ETHYLENE GLYCOL
Crystal Properties Matthews coefficient Solvent content 1.75 29.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.37 α = 90 b = 48.37 β = 90 c = 75.611 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 MARRESEARCH 2006-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
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 1.8 48.39 99 0.04 21.9 6.6 8738
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 1.8 1.9 100 0.57 2.3 5.5
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 1I92, 1G90 1.8 40.76 8204 489 98.7 0.205 0.201 0.2101 0.28 0.2961 RANDOM 38.92
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] 1.02 1.02 -2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.182 r_dihedral_angle_3_deg 14.581 r_dihedral_angle_4_deg 12.275 r_scangle_it 10.017 r_scbond_it 8.366 r_mcangle_it 6.384 r_dihedral_angle_1_deg 5.752 r_mcbond_it 4.859 r_angle_refined_deg 1.491 r_angle_other_deg 0.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.182 r_dihedral_angle_3_deg 14.581 r_dihedral_angle_4_deg 12.275 r_scangle_it 10.017 r_scbond_it 8.366 r_mcangle_it 6.384 r_dihedral_angle_1_deg 5.752 r_mcbond_it 4.859 r_angle_refined_deg 1.491 r_angle_other_deg 0.887 r_nbd_refined 0.213 r_symmetry_vdw_other 0.206 r_nbd_other 0.19 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.121 r_chiral_restr 0.098 r_nbtor_other 0.088 r_symmetry_hbond_refined 0.08 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001 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 679 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing