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Crystal structure of the third PDZ domain of human ligand-of-numb protein-X (LNX1) in complex with the C-terminal peptide from the coxsackievirus and adenovirus receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AWW PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L experimental model PDB 2BYG PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L experimental model PDB 2AWX PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L experimental model PDB 2AWU PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L experimental model PDB 2G2L PDB entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 293 1.53M Potassium phosphate, 0.27M Sodium phosphate, 1% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.782 α = 90 b = 58.449 β = 90 c = 73.741 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 2007-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99975 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 1.75 33.71 100 0.094 0.094 16 7.2 22359 22359 20.4
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 1.75 1.84 100 0.844 0.844 2.9 7.3 23287
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 entries 2AWW, 2BYG, 2AWX, 2AWU, 2G2L 1.75 33.71 21214 21214 1144 99.92 0.17657 0.17657 0.175 0.181 0.20529 0.2133 RANDOM 17.652
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] 0.56 -0.88 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.772 r_dihedral_angle_3_deg 11.648 r_scangle_it 10.02 r_dihedral_angle_4_deg 9.689 r_scbond_it 7.164 r_dihedral_angle_1_deg 5.877 r_mcangle_it 5.194 r_mcbond_it 3.711 r_angle_other_deg 1.913 r_mcbond_other 1.566
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.772 r_dihedral_angle_3_deg 11.648 r_scangle_it 10.02 r_dihedral_angle_4_deg 9.689 r_scbond_it 7.164 r_dihedral_angle_1_deg 5.877 r_mcangle_it 5.194 r_mcbond_it 3.711 r_angle_other_deg 1.913 r_mcbond_other 1.566 r_angle_refined_deg 1.404 r_symmetry_vdw_other 0.315 r_symmetry_vdw_refined 0.207 r_nbd_other 0.196 r_nbd_refined 0.188 r_symmetry_hbond_refined 0.169 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.088 r_nbtor_other 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1513 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling PHASER phasing