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Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with phosphorylated Syndecan1 Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KZD PDB ENTRY 3KZD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 291 0.1 M sodium acetate, 25% PEG4000, 8% isopropanol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.72 28.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 26.717 α = 90 b = 50.135 β = 90 c = 57.712 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 NOIR-1 2010-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.000 ALS 4.2.2
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 1.54 37.85 95.5 0.03 34.4 6.4 11979 11440 -3 13
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) 1 1.54 1.62 74.6 0.121 9.3 3.8 1685
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 PDB ENTRY 3KZD 1.54 37.85 10862 10862 546 95.04 0.16717 0.16717 0.16551 0.1652 0.19964 0.2041 RANDOM 13.551
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] 0.11 -0.08 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.693 r_dihedral_angle_4_deg 17.547 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_1_deg 6.231 r_scangle_it 4.174 r_scbond_it 2.648 r_mcangle_it 1.646 r_angle_refined_deg 1.265 r_rigid_bond_restr 1.111 r_mcbond_it 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.693 r_dihedral_angle_4_deg 17.547 r_dihedral_angle_3_deg 12.195 r_dihedral_angle_1_deg 6.231 r_scangle_it 4.174 r_scbond_it 2.648 r_mcangle_it 1.646 r_angle_refined_deg 1.265 r_rigid_bond_restr 1.111 r_mcbond_it 0.92 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 787 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 19
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling