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Crystal structure of NaLdpA mutant H97Q in complex with erythro-DGPD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7XXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% PEG 500 MME,
10% PEG 20000,
0.03 M MgCl2,
0.03 M CaCl2,
0.1 M Imidazole/MES buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.384 α = 90 b = 66.002 β = 108.675 c = 107.051 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 2020-10-22 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 1.661 56.234 94 0.087 0.036 0.999 12.8 7 69923
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 1.661 1.804 55.1 1.144 0.467 0.653 1.6 6.9
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 7XXX 1.661 56.234 69923 3285 79.105 0.169 0.167 0.1671 0.2009 0.2009 30.674
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] 0.197 0.14 -0.037 -0.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.549 r_dihedral_angle_4_deg 15.836 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_1_deg 7.385 r_lrange_it 6.265 r_lrange_other 6.035 r_scangle_it 3.918 r_scangle_other 3.917 r_mcangle_it 3.36 r_mcangle_other 3.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.549 r_dihedral_angle_4_deg 15.836 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_1_deg 7.385 r_lrange_it 6.265 r_lrange_other 6.035 r_scangle_it 3.918 r_scangle_other 3.917 r_mcangle_it 3.36 r_mcangle_other 3.36 r_scbond_it 2.509 r_scbond_other 2.509 r_mcbond_it 2.175 r_mcbond_other 2.175 r_angle_refined_deg 1.701 r_angle_other_deg 1.461 r_symmetry_xyhbond_nbd_refined 0.253 r_nbd_refined 0.214 r_nbd_other 0.208 r_symmetry_xyhbond_nbd_other 0.196 r_xyhbond_nbd_refined 0.19 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.179 r_symmetry_nbd_refined 0.117 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_2 0.073 r_ncsr_local_group_3 0.07 r_ncsr_local_group_1 0.067 r_xyhbond_nbd_other 0.045 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5709 Nucleic Acid Atoms Solvent Atoms 647 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction STARANISO data scaling MOLREP phasing