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Crystal structure of the C890S mutant of the 4th PDZ domain of human membrane associated guanylate kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I04 PDB entries 2I04,2PNT,2OPG experimental model PDB 2PNT PDB entries 2I04,2PNT,2OPG experimental model PDB 2OPG PDB entries 2I04,2PNT,2OPG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 1:2 Protein:Well solution ratio, 20% PEG 3350, 10% Ethylene glycol, 200 mM Sodium acetate, 100 mM BTP pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2 38.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.821 α = 90 b = 44.085 β = 90 c = 54.512 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 IMAGE PLATE RIGAKU RAXIS HTC OSMIC 2007-06-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2 23 96.9 0.069 0.075 27.8 7 5689 5434 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 2 2.11 95.1 0.29 0.313 5.7 7.2 759
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 2I04,2PNT,2OPG 2 20.97 5434 5230 252 96.24 0.17021 0.16722 0.1802 0.23313 0.2342 RANDOM 23.589
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] -0.01 -0.67 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.93 r_dihedral_angle_4_deg 12.89 r_dihedral_angle_3_deg 11.276 r_dihedral_angle_1_deg 5.684 r_scangle_it 4.95 r_scbond_it 3.267 r_mcangle_it 1.862 r_mcbond_it 1.23 r_angle_refined_deg 0.955 r_angle_other_deg 0.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.93 r_dihedral_angle_4_deg 12.89 r_dihedral_angle_3_deg 11.276 r_dihedral_angle_1_deg 5.684 r_scangle_it 4.95 r_scbond_it 3.267 r_mcangle_it 1.862 r_mcbond_it 1.23 r_angle_refined_deg 0.955 r_angle_other_deg 0.831 r_mcbond_other 0.266 r_symmetry_vdw_other 0.254 r_nbd_refined 0.181 r_nbd_other 0.17 r_nbtor_refined 0.16 r_symmetry_vdw_refined 0.099 r_xyhbond_nbd_refined 0.084 r_nbtor_other 0.075 r_chiral_restr 0.06 r_symmetry_hbond_refined 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 688 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection MOSFLM data reduction SCALA data scaling PHASER phasing