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Crystal Structure of the HtrA3 PDZ Domain Bound to a Phage-Derived Ligand (FGRWV)
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 6.5 292 0.1 M Bis-Tris, 0.2 M MgCl2, and 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, temperature 292K
Crystal Properties Matthews coefficient Solvent content 2.19 43.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.001 α = 90 b = 73.001 β = 90 c = 80.058 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 CCD ADSC QUANTUM 210 2004-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 1.00 ALS 5.0.1
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 1.7 50 99.9 0.049 12.8 7.6 24442 20.3
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 1.7 1.76 99.6 0.461 3.3 5.6 2354
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.7 30 24383 1224 99.93 0.184 0.182 0.1946 0.22 0.2314 RANDOM 20.507
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] 0.39 0.39 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.621 r_dihedral_angle_4_deg 16.898 r_dihedral_angle_3_deg 12.865 r_dihedral_angle_1_deg 6.021 r_scangle_it 5.593 r_scbond_it 3.889 r_mcangle_it 3.653 r_mcbond_it 2.975 r_angle_refined_deg 1.434 r_angle_other_deg 0.791
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.621 r_dihedral_angle_4_deg 16.898 r_dihedral_angle_3_deg 12.865 r_dihedral_angle_1_deg 6.021 r_scangle_it 5.593 r_scbond_it 3.889 r_mcangle_it 3.653 r_mcbond_it 2.975 r_angle_refined_deg 1.434 r_angle_other_deg 0.791 r_mcbond_other 0.585 r_symmetry_vdw_other 0.206 r_nbd_refined 0.204 r_nbd_other 0.182 r_nbtor_refined 0.164 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.084 r_nbtor_other 0.078 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1632 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing