☰ Navigation Tabs
Crystal structure of TnmS3 in complex with riboflavin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5UMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 100 mM ammonium acetate, 100 mM bis-tris, and 17% w/v polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 1.94 36.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.059 α = 90 b = 60.915 β = 90 c = 85.659 γ = 90
Symmetry Space Group P 21 21 21
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 6M 2016-03-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97926 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.59 40 99.2 0.071 0.078 0.031 0.996 23.7 5.7 39567
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.59 1.63 99.9 0.681 0.75 0.31 0.837 5.6 1976
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 5UMP 1.59 40 30454 1594 98.79 0.16618 0.16471 0.1755 0.19328 0.2068 RANDOM 16.617
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] 0.09 -0.04 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.847 r_dihedral_angle_3_deg 10.268 r_dihedral_angle_4_deg 8.685 r_dihedral_angle_1_deg 6.046 r_long_range_B_refined 4.487 r_long_range_B_other 4.313 r_scangle_other 2.655 r_mcangle_it 1.892 r_mcangle_other 1.892 r_scbond_it 1.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.847 r_dihedral_angle_3_deg 10.268 r_dihedral_angle_4_deg 8.685 r_dihedral_angle_1_deg 6.046 r_long_range_B_refined 4.487 r_long_range_B_other 4.313 r_scangle_other 2.655 r_mcangle_it 1.892 r_mcangle_other 1.892 r_scbond_it 1.657 r_scbond_other 1.656 r_angle_refined_deg 1.477 r_mcbond_it 1.108 r_mcbond_other 1.103 r_angle_other_deg 0.94 r_chiral_restr 0.081 r_bond_refined_d 0.01 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1856 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement MOLREP phasing HKL-3000 data reduction HKL-3000 data scaling