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Crystal structure of SpLdpA in complex with threo-DGPD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other NaLdpA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG 6000,
0.2 M MgCl2,
0.1 M HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 1.99 38.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.983 α = 90 b = 69.983 β = 90 c = 85.892 γ = 120
Symmetry Space Group P 3 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 2021-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.711 86.085 94.7 0.166 0.038 0.999 12.9 20.2 22162
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.711 1.85 55.8 2.398 0.549 0.623 1.5 19.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE NaLdpA 1.83 85.892 16207 706 73.682 0.178 0.176 0.1843 0.2289 0.2361 32.791
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] 0.227 0.113 0.227 -0.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.661 r_dihedral_angle_3_deg 15.838 r_dihedral_angle_4_deg 15.101 r_dihedral_angle_1_deg 7.48 r_lrange_it 5.478 r_lrange_other 5.446 r_scangle_it 2.805 r_scangle_other 2.804 r_mcangle_it 2.21 r_mcangle_other 2.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.661 r_dihedral_angle_3_deg 15.838 r_dihedral_angle_4_deg 15.101 r_dihedral_angle_1_deg 7.48 r_lrange_it 5.478 r_lrange_other 5.446 r_scangle_it 2.805 r_scangle_other 2.804 r_mcangle_it 2.21 r_mcangle_other 2.21 r_scbond_it 2.121 r_scbond_other 2.12 r_angle_refined_deg 1.665 r_mcbond_it 1.365 r_angle_other_deg 1.355 r_mcbond_other 1.353 r_nbd_refined 0.22 r_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.181 r_nbd_other 0.179 r_nbtor_refined 0.177 r_symmetry_nbd_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.14 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1992 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing