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Structure of a PDZ-protease bound to a substrate-binding adaptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XNF 1XNF, 4QL6 experimental model PDB 4QL6 1XNF, 4QL6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 289 0.2 M Ammonium citrate, 14% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.95 58.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.594 α = 90 b = 146.726 β = 90 c = 148.429 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 RAYONIX MX300HE 2016-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.20 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.3 104.35 99.9 0.067 0.955 21.05 4.5 105941
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 100 0.682 0.817 4.6
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 1XNF, 4QL6 2.3 104.35 100514 5470 90.3 0.22 0.217 0.2197 0.271 0.2699 RANDOM 44.84
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 0.09 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.847 r_dihedral_angle_3_deg 23.142 r_dihedral_angle_4_deg 22.409 r_long_range_B_refined 8.427 r_long_range_B_other 8.405 r_scangle_other 5.692 r_mcangle_it 5.441 r_mcangle_other 5.441 r_angle_other_deg 3.797 r_scbond_it 3.631
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.847 r_dihedral_angle_3_deg 23.142 r_dihedral_angle_4_deg 22.409 r_long_range_B_refined 8.427 r_long_range_B_other 8.405 r_scangle_other 5.692 r_mcangle_it 5.441 r_mcangle_other 5.441 r_angle_other_deg 3.797 r_scbond_it 3.631 r_scbond_other 3.63 r_mcbond_it 3.604 r_mcbond_other 3.602 r_dihedral_angle_1_deg 2.703 r_angle_refined_deg 1.774 r_chiral_restr 0.193 r_bond_refined_d 0.026 r_gen_planes_refined 0.008 r_gen_planes_other 0.007 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14758 Nucleic Acid Atoms Solvent Atoms 946 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing Coot model building HKL-2000 data scaling