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High resolution structure of human histidine triad nucleotide-binding protein 1 (hHINT1)/AMP complex in a monoclinic space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KPF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 278 19% PEG 8000, 0.1M sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.08 40.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.421 α = 90 b = 46.449 β = 94.42 c = 64.034 γ = 90
Symmetry Space Group C 1 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 100 CCD MAR CCD 165 mm 2011-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8123 EMBL/DESY, HAMBURG X13
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 1.38 25.58 100 0.122 13.1 4.4 45932 45932 -3 11.2
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 1.38 1.45 84 0.291 3.4 2.8 5760
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1KPF 1.38 25.58 46364 43580 2320 99 0.12277 0.12277 0.12073 0.1268 0.16148 0.1698 RANDOM 17.709
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] 1.33 -0.02 -0.76 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.035 r_dihedral_angle_4_deg 14.196 r_dihedral_angle_3_deg 13.05 r_dihedral_angle_1_deg 5.793 r_scangle_it 4.208 r_scbond_it 3.027 r_mcangle_it 1.906 r_angle_refined_deg 1.479 r_rigid_bond_restr 1.44 r_mcbond_it 1.219
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.035 r_dihedral_angle_4_deg 14.196 r_dihedral_angle_3_deg 13.05 r_dihedral_angle_1_deg 5.793 r_scangle_it 4.208 r_scbond_it 3.027 r_mcangle_it 1.906 r_angle_refined_deg 1.479 r_rigid_bond_restr 1.44 r_mcbond_it 1.219 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1767 Nucleic Acid Atoms Solvent Atoms 409 Heterogen Atoms 23
Software Software Software Name Purpose DNA data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling