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2.09 Angstrom resolution structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-1) from Bacillus anthracis str. 'Ames Ancestor' in complex with GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3H83
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 295 The Classics II Suite, condition B6, mixed at 1:1 v/v ratio with the protein at 7.4 mg/mL in 0.5 M NaCl, 5 mM BME, 1 mM GMP, 1 mM MgCl2, 10 mM Tris/HCl pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.8 56.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.22 α = 90 b = 80.477 β = 101.24 c = 120.236 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 2009-07-22 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 2.09 50 94 0.101 9.61 3.3 56550 56550 -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 2.09 2.13 99.5 0.539 2.66 3 2964
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 3H83 2.09 30.08 53702 53702 2830 93.92 0.20582 0.20385 0.216 0.2431 0.2563 RANDOM 24.226
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] -2.59 0.33 -1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.86 r_dihedral_angle_3_deg 10.261 r_dihedral_angle_4_deg 7.432 r_scangle_it 4.359 r_dihedral_angle_1_deg 3.23 r_scbond_it 2.944 r_mcangle_it 1.804 r_angle_refined_deg 1.696 r_mcbond_it 1.032 r_angle_other_deg 0.889
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.86 r_dihedral_angle_3_deg 10.261 r_dihedral_angle_4_deg 7.432 r_scangle_it 4.359 r_dihedral_angle_1_deg 3.23 r_scbond_it 2.944 r_mcangle_it 1.804 r_angle_refined_deg 1.696 r_mcbond_it 1.032 r_angle_other_deg 0.889 r_mcbond_other 0.306 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5921 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 190
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling