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Crystal structure of the 11th PDZ domain of MPDZ (MUPP1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HE2 PDB entries 2HE2, 1TP3 experimental model PDB 1TP3 PDB entries 2HE2, 1TP3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 293 0.8M (NH4)2SO4, 0.1M Citrate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.05 39.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.409 α = 90 b = 36.919 β = 90 c = 63.609 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 CCD MARMOSAIC 225 mm CCD 2007-02-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9182 SLS X10SA
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 1.4 31.8 96.6 0.073 0.073 13.5 4.6 15501 15501
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) 1.4 1.48 94.7 0.394 0.394 2.6 3.8 8319
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 2HE2, 1TP3 1.4 31.8 14686 14686 780 96.16 0.17252 0.17252 0.16937 0.23418 0.2576 RANDOM 14.93
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] 0.72 -1.84 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.514 r_dihedral_angle_4_deg 15.867 r_sphericity_free 12.968 r_dihedral_angle_3_deg 12.69 r_scangle_it 9.261 r_scbond_it 7.792 r_sphericity_bonded 6.723 r_mcangle_it 6.359 r_dihedral_angle_1_deg 5.724 r_mcbond_it 5.557
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.514 r_dihedral_angle_4_deg 15.867 r_sphericity_free 12.968 r_dihedral_angle_3_deg 12.69 r_scangle_it 9.261 r_scbond_it 7.792 r_sphericity_bonded 6.723 r_mcangle_it 6.359 r_dihedral_angle_1_deg 5.724 r_mcbond_it 5.557 r_rigid_bond_restr 4.205 r_mcbond_other 3.847 r_angle_refined_deg 1.489 r_angle_other_deg 0.865 r_symmetry_vdw_refined 0.259 r_symmetry_vdw_other 0.23 r_symmetry_hbond_refined 0.222 r_nbd_refined 0.208 r_nbd_other 0.194 r_nbtor_refined 0.162 r_xyhbond_nbd_refined 0.162 r_nbtor_other 0.09 r_chiral_restr 0.086 r_bond_refined_d 0.014 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 667 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing