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Crystal Structure of Free T-cell Lymphoma Invasion and Metastasis-1 PDZ Domain Quadruple Mutant (QM)
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 1.5M Ammonium Sulfate, 0.1M Tris, pH=8.5, 12% Glycerol, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.12 42.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.843 α = 90 b = 45.843 β = 90 c = 71.362 γ = 120
Symmetry Space Group P 32 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2011-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.5418
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 2.3 19.85 93.9 0.104 7.7 3.18 4117 3866 34.3
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 2.3 2.38 97.3 0.421 2.1 3.17
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 entry 3KZD 2.3 19.85 3958 3697 168 93.4 0.21873 0.21693 0.25777 0.2817 RANDOM 31.409
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] 9.21 9.21 -18.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.23 r_dihedral_angle_4_deg 24.499 r_dihedral_angle_3_deg 17.376 r_dihedral_angle_1_deg 5.571 r_long_range_B_refined 4.807 r_mcangle_it 1.797 r_scbond_it 1.129 r_angle_refined_deg 1.098 r_mcbond_it 0.998 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.23 r_dihedral_angle_4_deg 24.499 r_dihedral_angle_3_deg 17.376 r_dihedral_angle_1_deg 5.571 r_long_range_B_refined 4.807 r_mcangle_it 1.797 r_scbond_it 1.129 r_angle_refined_deg 1.098 r_mcbond_it 0.998 r_chiral_restr 0.066 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 666 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling