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Crystal Structure of the HtrA2/Omi PDZ Domain Bound to a Phage-Derived Ligand (WTMFWV)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LCY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 292 0.1 M sodium citrate, 1.0 M monoammonium dihydrogen phosphate, pH 5.6, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 3.36 63.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.105 α = 90 b = 90.105 β = 90 c = 83.516 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.975 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.75 50 99.8 0.071 11.2 6.9 9406
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.85 100 0.594 3.6 7.2 901
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 1LCY 2.75 20 8900 8898 453 99.98 0.21 0.208 0.2117 0.254 0.2499 RANDOM 35.281
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] -0.47 -0.47 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.386 r_scangle_it 3.977 r_mcangle_it 3.788 r_scbond_it 2.518 r_mcbond_it 2.279 r_angle_refined_deg 1.218 r_angle_other_deg 0.768 r_nbd_other 0.221 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.185
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.386 r_scangle_it 3.977 r_mcangle_it 3.788 r_scbond_it 2.518 r_mcbond_it 2.279 r_angle_refined_deg 1.218 r_angle_other_deg 0.768 r_nbd_other 0.221 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.185 r_symmetry_vdw_other 0.172 r_xyhbond_nbd_refined 0.087 r_nbtor_other 0.084 r_chiral_restr 0.067 r_bond_refined_d 0.012 r_symmetry_hbond_refined 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1678 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction AMoRE phasing