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Crystal Structure of Histidinol-phosphate aminotransferase from Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FG7 pdb entry 1fg7A as per Morda
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 287 Anatract/Microlytic MCSG1 screen, condition B6: 200mM Calcium acetate, 100mM MES / NaOH pH 6.0: 25% (w/V) PEG 8000: KlpnC.00674.a.B1.PW39002 at 33.5mg/ml: over night soak with 2.5mM PLP in DMSO: tra: 322257 b6: cryo: 20% EG + soak: puck: jql0-1.
Crystal Properties Matthews coefficient Solvent content 2.29 46.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.4 α = 90 b = 111.61 β = 90 c = 119.32 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 RAYONIX MX-300 Beryllium Lenses 2021-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.8 50 98.3 0.05 0.055 0.999 23.28 6.178 129492 27.82
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 94.7 0.42 0.463 0.9 3.64 5.687
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE pdb entry 1fg7A as per Morda 1.8 44.55 1.35 129462 2035 98.28 0.1519 0.1512 0.1583 0.193 0.2001 0 26.62
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.7596 f_angle_d 0.9101 f_chiral_restr 0.0592 f_plane_restr 0.0098 f_bond_d 0.0079
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10704 Nucleic Acid Atoms Solvent Atoms 1517 Heterogen Atoms 138
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MoRDa phasing PHENIX model building Coot model building