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The Crystal Structure of the Second PDZ Domain of Human DLG3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BYG 2BYG.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 Ammonium sulphate, Glycerol, Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.78 30.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.487 α = 90 b = 40.242 β = 92.8 c = 33.34 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 MARMOSAIC 225 mm CCD 2005-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97910 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.1 26.45 98.4 27971
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.1 1.16 96.6
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 (All) 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 2BYG.pdb 1.1 26.45 26547 26547 1406 98.11 0.11512 0.11512 0.11322 0.1153 0.15038 0.1117 RANDOM 7.076
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] 0.23 0.15 0.1 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.642 r_dihedral_angle_3_deg 12.6 r_dihedral_angle_4_deg 12.292 r_sphericity_free 8.369 r_dihedral_angle_1_deg 6.347 r_scangle_it 6.059 r_scbond_it 4.751 r_sphericity_bonded 4.091 r_mcangle_it 3.634 r_mcbond_it 3.211
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.642 r_dihedral_angle_3_deg 12.6 r_dihedral_angle_4_deg 12.292 r_sphericity_free 8.369 r_dihedral_angle_1_deg 6.347 r_scangle_it 6.059 r_scbond_it 4.751 r_sphericity_bonded 4.091 r_mcangle_it 3.634 r_mcbond_it 3.211 r_rigid_bond_restr 2.087 r_mcbond_other 1.813 r_angle_refined_deg 1.439 r_angle_other_deg 0.873 r_symmetry_vdw_refined 0.304 r_symmetry_vdw_other 0.278 r_symmetry_hbond_refined 0.233 r_nbd_refined 0.2 r_nbd_other 0.182 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.163 r_chiral_restr 0.09 r_nbtor_other 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 698 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing