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Tim-4 in complex with sodium potassium tartrate
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 7.5 294 0.1 M Hepes, 0.8 M potassium sodium tartrate tetrahydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 3.28 62.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.77 α = 90 b = 67.77 β = 90 c = 129.09 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 4 2006-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 2.05 25 99.9 0.063 0.063 9.5 19.7 11718 11714 27.9
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 2.16 99.6 0.302 2.5 15.4 1643
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 2.2 15 9009 449 100 0.21857 0.2176 0.2184 0.23782 0.2387 RANDOM 25.429
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] 1.47 0.74 1.47 -2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.837 r_dihedral_angle_4_deg 15.698 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_1_deg 6.64 r_scangle_it 2.413 r_scbond_it 1.358 r_angle_refined_deg 1.103 r_mcangle_it 1.054 r_mcbond_it 0.551 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.837 r_dihedral_angle_4_deg 15.698 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_1_deg 6.64 r_scangle_it 2.413 r_scbond_it 1.358 r_angle_refined_deg 1.103 r_mcangle_it 1.054 r_mcbond_it 0.551 r_nbtor_refined 0.299 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.109 r_symmetry_hbond_refined 0.095 r_metal_ion_refined 0.091 r_chiral_restr 0.08 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 864 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing