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1.98 Angstrom resolution crystal structure of a hypoxanthine-guanine phosphoribosyltransferase (hpt-2) from Bacillus anthracis str. 'Ames Ancestor'
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 5.5 293 protein at 7.4 mg/mL in 10 mM Tris/HCl, pH 8.3, 500 mM NaCl, 5 mM BME. Crystals grew from 2 M AmSO4 0.1 M bis-Tris pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.66 53.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.499 α = 90 b = 122.499 β = 90 c = 119.685 γ = 90
Symmetry Space Group P 41 21 2
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 225 mm CCD Be-Lenses/Diamond Laue Mono 2010-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97857 APS 21-ID-F
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 1.98 30 100 0.08 31.29 13 63787 63787 -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) 1.98 2.01 100 0.56 5.15 13.2 3146
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 1.98 29.92 60480 60480 3231 99.95 0.16918 0.16723 0.2004 0.20595 0.233 RANDOM 33.827
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] -0.42 -0.42 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.512 r_dihedral_angle_4_deg 11.62 r_dihedral_angle_3_deg 11.135 r_scangle_it 4.391 r_dihedral_angle_1_deg 3.783 r_scbond_it 2.646 r_mcangle_it 1.634 r_angle_refined_deg 1.581 r_mcbond_it 0.884 r_angle_other_deg 0.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.512 r_dihedral_angle_4_deg 11.62 r_dihedral_angle_3_deg 11.135 r_scangle_it 4.391 r_dihedral_angle_1_deg 3.783 r_scbond_it 2.646 r_mcangle_it 1.634 r_angle_refined_deg 1.581 r_mcbond_it 0.884 r_angle_other_deg 0.812 r_mcbond_other 0.248 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5330 Nucleic Acid Atoms Solvent Atoms 558 Heterogen Atoms 73
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling