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Crystal structure of Apo hypoxanthine-guanine phosphoribosyltransferase from Legionella pneumophila
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HGX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 289 0.2M Trimethylamine N-oxide dihydrate, 0.1M Tris pH 8.5, 20% w/v Polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.43 49.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.02 α = 90 b = 67.892 β = 90 c = 94.789 γ = 90
Symmetry Space Group P 21 21 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 CCD ADSC QUANTUM 315r 2014-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 99.7 17.3 7.1 17207
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 2.4 2.44 100 0.384 7.4 7.3
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 (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 1HGX 2.4 30 16293 869 99.4 0.16782 0.16532 0.1711 0.21885 0.2213 RANDOM 40.604
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] 2.87 0.79 -3.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.866 r_dihedral_angle_3_deg 18.196 r_dihedral_angle_4_deg 16.182 r_dihedral_angle_1_deg 6.155 r_angle_other_deg 3.581 r_angle_refined_deg 1.627 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_other 0.012 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.866 r_dihedral_angle_3_deg 18.196 r_dihedral_angle_4_deg 16.182 r_dihedral_angle_1_deg 6.155 r_angle_other_deg 3.581 r_angle_refined_deg 1.627 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_other 0.012 r_gen_planes_refined 0.007 r_bond_other_d 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2970 Nucleic Acid Atoms Solvent Atoms 97 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing