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Psychrobacter arcticus ATPPRT (HisGZ) R56A mutant bound to ATP and PRPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FU2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 8mg mL-1 protein (in 20mM Tris pH7, 50mM KCl, 10mM MgCl2, 2mM DTT, 0.5mM histidine) mixed in 1:1 ratio with precipitant solution (12% PEG3350, 100mM bicine pH8.5, 150mM SrCl2, 150mM KBr, 2% 1,6-hexanediol)
Crystal Properties Matthews coefficient Solvent content 2.48 50.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.155 α = 90 b = 145.525 β = 102.48 c = 93.812 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS EIGER2 XE 16M 2021-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.55 56.97 99.9 0.172 0.187 0.073 10.9 6.5 43754 53.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.55 2.59 99.3 3.175 3.424 1.274 0.8 7.1
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 6FU2 2.55 56.97 41555 2156 99.82 0.2351 0.233 0.2357 0.2753 0.2768 RANDOM 68.237
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] -2.42 -0.6 2.98 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.243 r_dihedral_angle_4_deg 16.815 r_dihedral_angle_3_deg 14.801 r_dihedral_angle_1_deg 6.797 r_angle_refined_deg 1.374 r_angle_other_deg 1.208 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.243 r_dihedral_angle_4_deg 16.815 r_dihedral_angle_3_deg 14.801 r_dihedral_angle_1_deg 6.797 r_angle_refined_deg 1.374 r_angle_other_deg 1.208 r_chiral_restr 0.052 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8394 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement xia2 data scaling MOLREP phasing PDB_EXTRACT data extraction DIALS data reduction