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X-Ray Crystallographic Structure of hTrap1 N-terminal Domain-apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 2 micro liter hTRAP1N, 25 mg/ml, in 30 mM TrisHCl pH 8.5, 0.15
M NaCl, and 1 mM TCEP was mixed with an equal volume of reservoir
solution consisting of 100 mM HEPES pH 7.5, 100 mM CaCl2 , 23 percent PEG3350, 4 percent isopropanol, and 0.4 micro liter of 1 M LiCl2.
Crystal Properties Matthews coefficient Solvent content 2.78 55.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.25 α = 90 b = 65.25 β = 90 c = 233.372 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 93 CCD ADSC QUANTUM 315r 2013-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.82 77.79 99.4 0.053 14 6.7 52606
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 1.82 1.85 99.6 0.486 3.75 7
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 FREE R-VALUE 5F5R 1.82 77.79 49944 2662 99.47 0.18332 0.18166 0.1889 0.2145 0.2186 RANDOM 29.583
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] 0.75 0.38 0.75 -1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.569 r_dihedral_angle_4_deg 18.468 r_dihedral_angle_3_deg 14.691 r_scangle_it 9.607 r_dihedral_angle_1_deg 7.167 r_scbond_it 6.144 r_mcangle_it 3.851 r_mcbond_it 2.489 r_angle_refined_deg 0.835 r_chiral_restr 0.075
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.569 r_dihedral_angle_4_deg 18.468 r_dihedral_angle_3_deg 14.691 r_scangle_it 9.607 r_dihedral_angle_1_deg 7.167 r_scbond_it 6.144 r_mcangle_it 3.851 r_mcbond_it 2.489 r_angle_refined_deg 0.835 r_chiral_restr 0.075 r_gen_planes_refined 0.022 r_bond_refined_d 0.007 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_other r_long_range_B_refined 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 3162 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing