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Crystal structure of E.coli CDP-diacylglycerol pyrophosphatase (Cdh) complexed with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P06282-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 0.1M HEPES (pH 7.5), 0.2M sodium chloride, 25% polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 3.7 66.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.352 α = 90 b = 80.047 β = 94.608 c = 138.599 γ = 90
Symmetry Space Group P 1 21 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 EIGER X 9M 2025-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 1.00003 PAL/PLS 5C (4A)
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 2.002 46.093 91.7 0.17 0.183 0.067 0.997 7.4 7.3 19212 24.85
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 2.002 2.178 88.4 1.169 0.446 0.66 7.9
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.002 46.05 19212 1004 33.185 0.22 0.2185 0.2185 0.2528 0.2529 RANDOM 26.091
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] 0.131 -0.008 -0.123 -0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.571 r_dihedral_angle_6_deg 13.567 r_dihedral_angle_1_deg 6.896 r_lrange_it 6.781 r_dihedral_angle_2_deg 5.854 r_scangle_it 3.657 r_mcangle_it 2.992 r_scbond_it 2.123 r_angle_refined_deg 1.772 r_mcbond_it 1.696
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.571 r_dihedral_angle_6_deg 13.567 r_dihedral_angle_1_deg 6.896 r_lrange_it 6.781 r_dihedral_angle_2_deg 5.854 r_scangle_it 3.657 r_mcangle_it 2.992 r_scbond_it 2.123 r_angle_refined_deg 1.772 r_mcbond_it 1.696 r_nbtor_refined 0.279 r_symmetry_nbd_refined 0.179 r_nbd_refined 0.178 r_xyhbond_nbd_refined 0.146 r_chiral_restr 0.138 r_ncsr_local_group_1 0.077 r_symmetry_xyhbond_nbd_refined 0.059 r_gen_planes_refined 0.006 r_bond_refined_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3570 Nucleic Acid Atoms Solvent Atoms 94 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement autoPROC data processing MOLREP phasing Coot model building MxDC data collection PDB_EXTRACT data extraction STARANISO data scaling