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Human histidine triad nucleotide-binding protein 2 (hHINT2) refined to 2.11 A in C2221 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 6.5 281 0.2 M sodium citrate, 0.1 M sodium cacodylate, 30 % 2-propanol
Crystal Properties Matthews coefficient Solvent content 3.99 69.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.411 α = 90 b = 153.992 β = 90 c = 74.785 γ = 90
Symmetry Space Group C 2 2 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 2013-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9669 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 2.11 102.94 99.6 0.22 0.24 0.094 0.994 11.3 12.2 46164 15.482
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 2.11 2.17 96.4 1.041 1.194 0.568 0.697 2 7.4
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 2.11 102.94 46144 2349 99.59 0.149 0.1476 0.1616 0.1845 0.194 25.345
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] 0.105 1.922 -2.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.528 r_dihedral_angle_4_deg 19.916 r_dihedral_angle_3_deg 13.285 r_lrange_it 7.575 r_lrange_other 7.256 r_dihedral_angle_1_deg 6.592 r_scangle_it 4.936 r_scangle_other 4.935 r_scbond_it 3.242 r_scbond_other 3.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.528 r_dihedral_angle_4_deg 19.916 r_dihedral_angle_3_deg 13.285 r_lrange_it 7.575 r_lrange_other 7.256 r_dihedral_angle_1_deg 6.592 r_scangle_it 4.936 r_scangle_other 4.935 r_scbond_it 3.242 r_scbond_other 3.242 r_mcangle_it 2.988 r_mcangle_other 2.988 r_mcbond_it 2.021 r_mcbond_other 2.018 r_angle_refined_deg 1.613 r_angle_other_deg 1.407 r_nbd_refined 0.229 r_nbd_other 0.207 r_symmetry_xyhbond_nbd_refined 0.201 r_xyhbond_nbd_refined 0.185 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.158 r_symmetry_nbd_refined 0.136 r_ncsr_local_group_1 0.092 r_chiral_restr 0.088 r_ncsr_local_group_6 0.086 r_ncsr_local_group_3 0.085 r_ncsr_local_group_5 0.083 r_symmetry_nbtor_other 0.081 r_ncsr_local_group_2 0.081 r_ncsr_local_group_4 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3532 Nucleic Acid Atoms Solvent Atoms 674 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing