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Crystal structure of AtTTM3 in complex with tripolyphosphate and manganese ion (form B)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A5Y PDB ENTRY 5A5Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 20 % PEG 3350,0.2M NACL, 0.1 M BISTRIS PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.22 44.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.375 α = 90 b = 33.868 β = 94.97 c = 72.216 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M-F 2015-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000020, 1.823310 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.3 19.6 98.3 0.05 20.04 6.24 52725 -3
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 1.3 1.37 93.3 0.77 1.94 5.27
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 5A5Y 1.3 19.61 50172 2541 98.31 0.14211 0.14044 0.17542 0.1816 RANDOM 18.715
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] -1.24 1.57 -0.33
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.158 r_dihedral_angle_2_deg 31.646 r_dihedral_angle_4_deg 16.18 r_sphericity_bonded 12.438 r_dihedral_angle_3_deg 12.377 r_dihedral_angle_1_deg 6.107 r_scbond_it 2.433 r_mcangle_it 2.09 r_rigid_bond_restr 1.818 r_angle_refined_deg 1.695
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 44.158 r_dihedral_angle_2_deg 31.646 r_dihedral_angle_4_deg 16.18 r_sphericity_bonded 12.438 r_dihedral_angle_3_deg 12.377 r_dihedral_angle_1_deg 6.107 r_scbond_it 2.433 r_mcangle_it 2.09 r_rigid_bond_restr 1.818 r_angle_refined_deg 1.695 r_mcbond_it 1.628 r_mcbond_other 1.618 r_angle_other_deg 0.913 r_chiral_restr 0.103 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1674 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing