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Crystal structure of the 3rd PDZ domain of human membrane associated guanylate kinase, C677S and C709S double mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UJV PDB entries 1UJV, 1G9O experimental model PDB 1G9O PDB entries 1UJV, 1G9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 293 0.05M Zn acetate pH 6.2, 30% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.1 41.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.472 α = 90 b = 61.578 β = 90 c = 80.113 γ = 90
Symmetry Space Group C 2 2 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 MARRESEARCH 2007-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97912 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 1.6 40.06 99.9 0.074 0.03 17.1 7.1 10994 10446 2
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 1.6 1.69 99.7 0.898 0.346 2.2 7.1 1571
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 (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 entries 1UJV, 1G9O 1.6 28.74 10446 10446 515 99.96 0.20418 0.20202 0.2107 0.25112 0.2549 RANDOM 15.883
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] 2.32 -0.12 -2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.389 r_dihedral_angle_3_deg 11.723 r_dihedral_angle_4_deg 10.265 r_scangle_it 8.178 r_scbond_it 6.953 r_dihedral_angle_1_deg 5.983 r_mcangle_it 4.862 r_mcbond_it 3.592 r_angle_refined_deg 1.597 r_mcbond_other 1.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.389 r_dihedral_angle_3_deg 11.723 r_dihedral_angle_4_deg 10.265 r_scangle_it 8.178 r_scbond_it 6.953 r_dihedral_angle_1_deg 5.983 r_mcangle_it 4.862 r_mcbond_it 3.592 r_angle_refined_deg 1.597 r_mcbond_other 1.084 r_angle_other_deg 0.916 r_chiral_restr 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 630 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing