☰ Navigation Tabs
Crystal Structure of the MurT/GatD Enzyme Complex from Streptococcus pyogenes with bound AMPPNP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9SQ9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 17% (w/v) PEG 3350
0.2 M HEPES pH 7.0
0.2 M NaCl
Crystal Properties Matthews coefficient Solvent content 2.52 51.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.289 α = 90 b = 101.21 β = 90 c = 177.296 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 PIXEL DECTRIS EIGER2 X 16M 2023-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.03321 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.981 49.112 99.55 0.1669 0.1756 0.05389 0.998 11.12 10.3 110500
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.981 2.051 99.14 0.703 0.474 1.05 10.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.981 49.112 110497 1547 99.559 0.181 0.1803 0.1896 0.2173 0.2358 49.396
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] -1.497 1.3 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.995 r_dihedral_angle_4_deg 20.896 r_dihedral_angle_3_deg 13.829 r_lrange_it 8.157 r_lrange_other 8.156 r_dihedral_angle_1_deg 7.118 r_scangle_it 6.808 r_scangle_other 6.808 r_scbond_it 4.942 r_scbond_other 4.941
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.995 r_dihedral_angle_4_deg 20.896 r_dihedral_angle_3_deg 13.829 r_lrange_it 8.157 r_lrange_other 8.156 r_dihedral_angle_1_deg 7.118 r_scangle_it 6.808 r_scangle_other 6.808 r_scbond_it 4.942 r_scbond_other 4.941 r_mcangle_other 4.848 r_mcangle_it 4.847 r_mcbond_it 3.672 r_mcbond_other 3.67 r_angle_other_deg 2.386 r_angle_refined_deg 1.593 r_chiral_restr_other 0.452 r_nbd_other 0.355 r_symmetry_nbd_refined 0.272 r_symmetry_nbd_other 0.216 r_symmetry_xyhbond_nbd_refined 0.211 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.169 r_nbtor_refined 0.167 r_xyhbond_nbd_other 0.133 r_chiral_restr 0.073 r_symmetry_nbtor_other 0.071 r_symmetry_xyhbond_nbd_other 0.069 r_bond_other_d 0.036 r_gen_planes_other 0.01 r_bond_refined_d 0.009 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10153 Nucleic Acid Atoms Solvent Atoms 719 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing