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Crystal structure of SpLdpA in complex with erythro-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 30% PEG 4000,
0.2 M lithium sulfate,
0.1 M Tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.24 45.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.281 α = 90 b = 71.281 β = 90 c = 86.922 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 2022-02-05 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 1.683 86.922 86.5 0.194 0.044 0.999 13.3 19.9 23171
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 1.683 1.782 58.7 2.506 0.587 0.599 1.4 19
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 1.683 86.922 23170 1147 78.441 0.149 0.148 0.1598 0.1768 0.1833 23.274
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] 0.046 0.023 0.046 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.54 r_dihedral_angle_3_deg 13.182 r_dihedral_angle_4_deg 11.4 r_dihedral_angle_1_deg 7.172 r_lrange_it 6.158 r_lrange_other 5.927 r_scangle_it 4.344 r_scangle_other 4.343 r_scbond_it 2.79 r_scbond_other 2.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.54 r_dihedral_angle_3_deg 13.182 r_dihedral_angle_4_deg 11.4 r_dihedral_angle_1_deg 7.172 r_lrange_it 6.158 r_lrange_other 5.927 r_scangle_it 4.344 r_scangle_other 4.343 r_scbond_it 2.79 r_scbond_other 2.789 r_mcangle_it 2.502 r_mcangle_other 2.501 r_angle_refined_deg 1.879 r_mcbond_other 1.68 r_mcbond_it 1.679 r_angle_other_deg 1.489 r_nbd_refined 0.212 r_nbd_other 0.201 r_symmetry_nbd_other 0.191 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.182 r_symmetry_nbd_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.16 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2005 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing