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DhhP of Borrelia burgdorferi in complex with MD1252
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 12.5% w/v PEG 4.000,
20% w/v 1,2,6-hexanetriol,
100mM BES/TEA pH 7.5,
10mM spermine tetrahydrochloride,
10mM spermidine trihydrochloride,
10mM 1,4-diaminobutane dihydrochloride,
10mM DL-ornithine monohydrochloride,
3% DMSO
Crystal Properties Matthews coefficient Solvent content 2.7 54.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.55 α = 91.92 b = 80.31 β = 90.99 c = 132.5 γ = 92.41
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 PILATUS 6M 2024-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
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 34.89 99.83 0.2842 0.3074 0.1163 0.99 6.24 6.9 61337 64.23
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 3.107 99.82 1.068 1.156 0.4385 0.512 1.99 6.8
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 34.89 1.98 61316 3067 99.88 0.2066 0.2049 0.2054 0.2381 0.2385 random selection 71.43
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 9.4275 f_angle_d 0.4765 f_chiral_restr 0.0421 f_plane_restr 0.0029 f_bond_d 0.0018
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20477 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 192
Software Software Software Name Purpose XDS data reduction XDS data scaling PHASER phasing PHENIX refinement Coot model building