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Crystal structures and thermostability of mutant TRAP3 A7 (ENGINEERED TRAP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EXS PDB ENTRY 2EXS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 0.1M sodium citrate pH5.5, 30%(w/v)MPD, 0.2M ammonium acetate, 10mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.137 α = 90 b = 110.137 β = 90 c = 36.976 γ = 90
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 190 mirrors 2007-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.000 Photon Factory BL-17A
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 1.8 50 94.7 0.08 0.062 10.7 4.3 39479 14.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.86 70.3 0.304 0.454 9 1.9 2921
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 PDB ENTRY 2EXS 1.8 20 37466 1975 100 0.19618 0.19377 0.194 0.244 0.2454 RANDOM 14.19
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.154 r_dihedral_angle_4_deg 16.287 r_dihedral_angle_3_deg 15.957 r_dihedral_angle_1_deg 7.53 r_scangle_it 4.073 r_scbond_it 2.634 r_mcangle_it 1.568 r_angle_refined_deg 1.477 r_mcbond_it 1.051 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.154 r_dihedral_angle_4_deg 16.287 r_dihedral_angle_3_deg 15.957 r_dihedral_angle_1_deg 7.53 r_scangle_it 4.073 r_scbond_it 2.634 r_mcangle_it 1.568 r_angle_refined_deg 1.477 r_mcbond_it 1.051 r_nbtor_refined 0.306 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.174 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.167 r_chiral_restr 0.111 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_refined 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 3213 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing