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DhhP of Borrelia burgdorferi in complex with AMP (SAD/Fe)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9R7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 20% v/v PEG 500 MME;
10% w/v PEG 20.000;
100mM Gly-Gly/AMPD pH 8.5;
0.3% w/v CHAPS;
0.3% w/v CHAPSO;
0.3% w/v Sodium glycocholate hydrate;
0.3% w/v Taurocholic acid sodium salt hydrate;
3% DMSO
Crystal Properties Matthews coefficient Solvent content 2.72 54.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.79 α = 91.1 b = 80.41 β = 91.33 c = 132.8 γ = 92.7
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 CdTe 16M 2025-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 1.735 PETRA III, EMBL c/o DESY P14 (MX2)
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 3.3 49.05 96.59 0.1177 0.1396 0.07402 0.994 11.34 3.4 89842 77.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.3 3.418 96.74 0.5454 0.6419 0.335 0.844 3.62 3.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.3 49.05 0.79 89805 4489 96.61 0.1772 0.1757 0.1733 0.2049 0.2005 random selection 82.15
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 10.1071 f_angle_d 0.5558 f_chiral_restr 0.0431 f_plane_restr 0.0038 f_bond_d 0.0029
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20431 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms 108
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing PHENIX refinement Coot model building