☰ Navigation Tabs
Crystal structure of PDZ1-2 from PSD-95
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RL7 3rl7, 3rl8 experimental model PDB 3RL8 3rl7, 3rl8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2 M calcium acetate; 0.1 M sodium cacodylate; 40% v/v PEG 400
Crystal Properties Matthews coefficient Solvent content 2.73 54.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.38 α = 90 b = 50.38 β = 90 c = 178.27 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 PIXEL DECTRIS PILATUS 2M 2014-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.920 Diamond I04
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 2.04 48.48 99.4 0.05 0.999 24.4 11.1 14015
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 2.04 2.09 97.6 0.547 0.851 2.8 5.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3rl7, 3rl8 2.04 48.48 13994 735 99.389 0.226 0.2244 0.2267 0.2597 0.2633 65.303
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] -0.256 -0.256 0.513
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.327 r_dihedral_angle_3_deg 11.507 r_dihedral_angle_4_deg 9.216 r_lrange_it 7.107 r_dihedral_angle_1_deg 5.223 r_scangle_it 2.889 r_mcangle_it 2.565 r_scbond_it 1.752 r_mcbond_it 1.436 r_angle_refined_deg 0.996
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.327 r_dihedral_angle_3_deg 11.507 r_dihedral_angle_4_deg 9.216 r_lrange_it 7.107 r_dihedral_angle_1_deg 5.223 r_scangle_it 2.889 r_mcangle_it 2.565 r_scbond_it 1.752 r_mcbond_it 1.436 r_angle_refined_deg 0.996 r_nbtor_refined 0.294 r_nbd_refined 0.179 r_symmetry_nbd_refined 0.166 r_symmetry_xyhbond_nbd_refined 0.132 r_xyhbond_nbd_refined 0.1 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1416 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction SCALA data scaling pointless data scaling PHASER phasing