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1.55 Angstrom Resolution Crystal Structure of 6-phosphogluconolactonase from Klebsiella pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4QRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 292 Protein: 9.8 mg/ml, 0.01M Tris-HCl pH 8.3,
Screen: PACT (F6), 0.2M Sodium formate, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.745 α = 90 b = 184.745 β = 90 c = 48.761 γ = 120
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 C(111) 2018-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.55 30 100 0.1 0.1 0.106 0.035 20.5 9.8 138516 -3 12.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.58 100 0.711 0.711 0.757 0.258 0.861 3.2 8.5
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 4QRJ 1.55 29.33 131376 6945 99.98 0.12721 0.12569 0.1398 0.15552 0.1662 RANDOM 12.521
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] 0.07 0.04 0.07 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.869 r_dihedral_angle_4_deg 17.193 r_dihedral_angle_3_deg 10.217 r_dihedral_angle_1_deg 5.515 r_long_range_B_refined 4.998 r_long_range_B_other 4.513 r_scangle_other 3.337 r_scbond_it 2.187 r_scbond_other 2.187 r_mcangle_it 1.426
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.869 r_dihedral_angle_4_deg 17.193 r_dihedral_angle_3_deg 10.217 r_dihedral_angle_1_deg 5.515 r_long_range_B_refined 4.998 r_long_range_B_other 4.513 r_scangle_other 3.337 r_scbond_it 2.187 r_scbond_other 2.187 r_mcangle_it 1.426 r_mcangle_other 1.426 r_angle_refined_deg 1.376 r_mcbond_it 0.97 r_mcbond_other 0.97 r_angle_other_deg 0.449 r_chiral_restr 0.07 r_gen_planes_refined 0.042 r_gen_planes_other 0.039 r_bond_refined_d 0.008 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7698 Nucleic Acid Atoms Solvent Atoms 1779 Heterogen Atoms 83
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing