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Crystal structures and thermostability of mutant TRAP3 A5 (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 10.5 293 0.09M CAPS pH 10.5, 30%(w/v) PEG300, 0.15M Ammonium sulfate, 10mM L-tryptophan, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.676 α = 90 b = 109.676 β = 90 c = 36.756 γ = 90
Symmetry Space Group P 4 21 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 210 mirrors 2006-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 50 95.7 0.061 0.048 12.3 5 7898 27.4
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 2.5 2.59 93.6 0.221 0.246 11.7 4.1 744
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 2.5 20 7503 363 100 0.19971 0.19691 0.1936 0.25647 0.2438 RANDOM 27.491
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] -0.35 -0.35 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.18 r_dihedral_angle_4_deg 17.298 r_dihedral_angle_3_deg 16.015 r_dihedral_angle_1_deg 7.103 r_scangle_it 3.034 r_scbond_it 1.855 r_angle_refined_deg 1.422 r_mcangle_it 1.235 r_mcbond_it 0.744 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.18 r_dihedral_angle_4_deg 17.298 r_dihedral_angle_3_deg 16.015 r_dihedral_angle_1_deg 7.103 r_scangle_it 3.034 r_scbond_it 1.855 r_angle_refined_deg 1.422 r_mcangle_it 1.235 r_mcbond_it 0.744 r_nbtor_refined 0.303 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.184 r_xyhbond_nbd_refined 0.148 r_symmetry_hbond_refined 0.129 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1519 Nucleic Acid Atoms Solvent Atoms 39 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling PHASER phasing