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Crystal structure of PSD-95 tandem PDZ domains 1 and 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2I1N PDB entries 2I1N, 2FE5 experimental model PDB 2FE5 PDB entries 2I1N, 2FE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 35% v/v 2-methyl-2,4-pentanediol, 0.1M Tris-HCl pH 7.0. 0.2M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.48 50.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.244 α = 90 b = 62.511 β = 99.25 c = 59.342 γ = 90
Symmetry Space Group P 1 21 1
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 270 Toroidal focusing mirror 2009-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 0.97000 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.05 50 98.1 0.058 21.2 3.7 26112 25616 35.16
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.05 2.12 96.3 0.349 3.1 3.6 2594
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries 2I1N, 2FE5 2.05 32.31 25616 25598 2576 98.09 0.2209 0.21412 0.28146 0.2939 RANDOM 37.914
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] -0.04 0.07 -1.18 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.674 r_dihedral_angle_3_deg 10.015 r_dihedral_angle_4_deg 9.212 r_scangle_it 8.465 r_scbond_it 5.924 r_dihedral_angle_1_deg 3.94 r_mcangle_it 3.827 r_mcbond_it 2.631 r_angle_refined_deg 0.631 r_symmetry_vdw_refined 0.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.674 r_dihedral_angle_3_deg 10.015 r_dihedral_angle_4_deg 9.212 r_scangle_it 8.465 r_scbond_it 5.924 r_dihedral_angle_1_deg 3.94 r_mcangle_it 3.827 r_mcbond_it 2.631 r_angle_refined_deg 0.631 r_symmetry_vdw_refined 0.331 r_nbtor_refined 0.328 r_nbd_refined 0.275 r_symmetry_hbond_refined 0.234 r_xyhbond_nbd_refined 0.196 r_chiral_restr 0.054 r_bond_refined_d 0.003 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2864 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling