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Tim-4 in complex with phosphatidylserine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OR7 TIM-2 HOMOLOGOUS MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 294 0.1 M SODIUM CITRATE, 10 % JEFFAMINE, 10 mM FeCl3. PROTEIN PRE-INCUBATED WITH 5 mM 1,2 DICAPROYL-sn-GLYCERO-3-(PHOSPHO-L-SERINE) AND 5 mM CaCl2, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.38 63.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.26 α = 90 b = 66.26 β = 90 c = 139.39 γ = 120
Symmetry Space Group P 63 2 2
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 315 2006-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97925 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 25 99.9 0.057 5.7 9.3 11 6801 6799
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) 2.5 2.64 100 0.168 4.4 10.2
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 (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 TIM-2 HOMOLOGOUS MODEL 2.5 15 6421 321 99.93 0.22082 0.21943 0.2215 0.24831 0.2503 RANDOM 36.021
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] 1.34 0.67 1.34 -2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.398 r_dihedral_angle_4_deg 18.573 r_dihedral_angle_3_deg 14.926 r_dihedral_angle_1_deg 6.214 r_rigid_bond_restr 6.153 r_scbond_it 5.219 r_scangle_it 4.125 r_sphericity_free 2.58 r_sphericity_bonded 2.283 r_mcangle_it 1.115
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.398 r_dihedral_angle_4_deg 18.573 r_dihedral_angle_3_deg 14.926 r_dihedral_angle_1_deg 6.214 r_rigid_bond_restr 6.153 r_scbond_it 5.219 r_scangle_it 4.125 r_sphericity_free 2.58 r_sphericity_bonded 2.283 r_mcangle_it 1.115 r_angle_refined_deg 1.114 r_mcbond_it 0.64 r_nbtor_refined 0.298 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.165 r_metal_ion_refined 0.148 r_symmetry_hbond_refined 0.111 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 855 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction SCALA data scaling PHASER phasing