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Crystal structure of a C1190S mutant of the 6th PDZ domain of human membrane associated guanylate kinase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JIK PDB entry 2JIK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 277 20% PEG 3350, 0.1M Citrate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.99 38.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.052 α = 90 b = 77.759 β = 101.49 c = 50.182 γ = 90
Symmetry Space Group P 1 21 1
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 2007-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.006029 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 2.05 39.25 92.6 0.133 0.133 9.1 3.1 17538 17538 22.2
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 2.05 2.16 99.8 0.683 0.683 2.1 3.1 8383
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2JIK 2.05 38.87 16559 16559 883 91.82 0.19148 0.19148 0.18781 0.1918 0.25829 0.2595 RANDOM 16.086
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] 0.33 0.13 -0.12 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.629 r_dihedral_angle_4_deg 18.747 r_dihedral_angle_3_deg 17.744 r_scangle_it 10.191 r_scbond_it 7.918 r_dihedral_angle_1_deg 6.252 r_mcangle_it 5.773 r_mcbond_it 5.197 r_mcbond_other 2.263 r_angle_refined_deg 1.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.629 r_dihedral_angle_4_deg 18.747 r_dihedral_angle_3_deg 17.744 r_scangle_it 10.191 r_scbond_it 7.918 r_dihedral_angle_1_deg 6.252 r_mcangle_it 5.773 r_mcbond_it 5.197 r_mcbond_other 2.263 r_angle_refined_deg 1.683 r_angle_other_deg 1.228 r_symmetry_vdw_other 0.239 r_symmetry_vdw_refined 0.211 r_nbd_other 0.196 r_nbd_refined 0.194 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.147 r_symmetry_hbond_refined 0.131 r_nbtor_other 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2091 Nucleic Acid Atoms Solvent Atoms 114 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing