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Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 1.41 A in P212121 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3TW2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 281 8 % w/v PEG8000, 0.1 M Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.921 α = 90 b = 74.113 β = 90 c = 77.249 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-F 2018-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.407 77.25 98.8 0.073 0.079 0.03 0.999 18.2 12.5 42522 11.6
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 1.407 1.43 75.7 0.715 0.846 0.439 0.755 2.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3TW2 1.407 53.48 42457 2092 98.673 0.102 0.1003 0.0999 0.1428 0.1425 17.947
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] -0.771 0.182 0.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.084 r_dihedral_angle_4_deg 16.681 r_dihedral_angle_3_deg 12.144 r_dihedral_angle_1_deg 6.291 r_scangle_it 5.603 r_scangle_other 5.602 r_rigid_bond_restr 5.325 r_lrange_it 5.219 r_scbond_it 5.21 r_scbond_other 5.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.084 r_dihedral_angle_4_deg 16.681 r_dihedral_angle_3_deg 12.144 r_dihedral_angle_1_deg 6.291 r_scangle_it 5.603 r_scangle_other 5.602 r_rigid_bond_restr 5.325 r_lrange_it 5.219 r_scbond_it 5.21 r_scbond_other 5.21 r_lrange_other 4.384 r_mcangle_it 2.463 r_mcangle_other 2.463 r_angle_refined_deg 2.008 r_mcbond_other 1.989 r_mcbond_it 1.988 r_angle_other_deg 1.665 r_nbd_refined 0.266 r_symmetry_nbd_other 0.201 r_symmetry_nbd_refined 0.191 r_nbd_other 0.189 r_xyhbond_nbd_refined 0.171 r_nbtor_refined 0.164 r_chiral_restr 0.142 r_symmetry_xyhbond_nbd_refined 0.109 r_symmetry_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.012 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1685 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing