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Crystal structure of PDZ1-2 from PSD-95 with peptide ligand sequence RRESEI bound to both domains
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 6.2 277 0.2 M NaCl, 0.1 M Na/K phosphate, 50% v/v PEG 200.
Matrix microseeding with Apo crystal form (PDB ID: 6spv).
Crystal Properties Matthews coefficient Solvent content 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.5 α = 90 b = 50.5 β = 90 c = 176.37 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 6M 2014-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.979 Diamond I04-1
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 2.08 48.55 100 0.075 0.998 14.5 7 13236
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 2.08 2.13 99.9 0.538 0.762 2.7 3.8
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 2.08 48.549 13216 703 99.97 0.203 0.2004 0.202 0.2399 0.2445 47.492
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] 0.226 0.226 -0.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.267 r_dihedral_angle_3_deg 12.131 r_dihedral_angle_4_deg 11.77 r_lrange_it 7.328 r_dihedral_angle_1_deg 5.46 r_scangle_it 3.253 r_mcangle_it 3.072 r_scbond_it 1.941 r_mcbond_it 1.754 r_angle_refined_deg 1.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.267 r_dihedral_angle_3_deg 12.131 r_dihedral_angle_4_deg 11.77 r_lrange_it 7.328 r_dihedral_angle_1_deg 5.46 r_scangle_it 3.253 r_mcangle_it 3.072 r_scbond_it 1.941 r_mcbond_it 1.754 r_angle_refined_deg 1.139 r_nbtor_refined 0.296 r_nbd_refined 0.19 r_symmetry_nbd_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.153 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.095 r_bond_refined_d 0.006 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1526 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction XDS data reduction SCALA data scaling pointless data scaling PHASER phasing