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12th PDZ domain of Multiple PDZ Domain Protein MPDZ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FNE PDB ENTRY 2FNE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 2M (NH4)2SO4, pH 7.50
Crystal Properties Matthews coefficient Solvent content 1.85 33.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.483 α = 90 b = 76.403 β = 90 c = 32.629 γ = 90
Symmetry Space Group P 21 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 2006-06-16 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 1.7 38.21 99.7 0.1 11 3.6 21145
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 1.79 100 0.43 3.1 3.6
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 2FNE 1.7 53.3 20020 1082 99.5 0.184 0.183 0.1907 0.215 0.2235 RANDOM 18.52
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] 0.18 -0.33 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.413 r_dihedral_angle_4_deg 27.81 r_dihedral_angle_3_deg 13.893 r_scangle_it 11.388 r_scbond_it 9.047 r_mcangle_it 5.993 r_dihedral_angle_1_deg 5.26 r_mcbond_it 4.372 r_angle_refined_deg 1.626 r_angle_other_deg 0.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.413 r_dihedral_angle_4_deg 27.81 r_dihedral_angle_3_deg 13.893 r_scangle_it 11.388 r_scbond_it 9.047 r_mcangle_it 5.993 r_dihedral_angle_1_deg 5.26 r_mcbond_it 4.372 r_angle_refined_deg 1.626 r_angle_other_deg 0.921 r_symmetry_vdw_refined 0.225 r_symmetry_vdw_other 0.206 r_nbd_other 0.201 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.174 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.15 r_chiral_restr 0.095 r_nbtor_other 0.087 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 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 1344 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing