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2.06 Angstrom resolution structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-1) from Bacillus anthracis str. 'Ames Ancestor'
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YFZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 The Classic II Suite, condition B6, mixed with 1:1 v/v with protein sample (7.4 mg/mL, 0.25 M NaCl, 5 mM BME, 10 mM Tris/HCl pH 8.3), VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.81 56.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.236 α = 90 b = 80.549 β = 101.23 c = 120.536 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 CCD MARMOSAIC 300 mm CCD Be Lenses/Diamond Laue Mono 2009-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.06 50 97 0.09 11.85 3.4 61007 61007 -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 2.06 2.1 99.9 0.255 4.4 3
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 (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 1YFZ 2.06 30 57870 57870 3105 96.74 0.1704 0.16841 0.1756 0.20753 0.2135 RANDOM 19.931
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] -1.56 -0.09 1.45 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.545 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_4_deg 10.979 r_scangle_it 6.34 r_dihedral_angle_1_deg 4.959 r_scbond_it 4.097 r_mcangle_it 2.65 r_angle_refined_deg 1.767 r_mcbond_it 1.477 r_angle_other_deg 0.987
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.545 r_dihedral_angle_3_deg 12.257 r_dihedral_angle_4_deg 10.979 r_scangle_it 6.34 r_dihedral_angle_1_deg 4.959 r_scbond_it 4.097 r_mcangle_it 2.65 r_angle_refined_deg 1.767 r_mcbond_it 1.477 r_angle_other_deg 0.987 r_mcbond_other 0.467 r_chiral_restr 0.185 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5895 Nucleic Acid Atoms Solvent Atoms 510 Heterogen Atoms 119
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling