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Structure of Enterococcus faecium CdaA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 1.5 M Lithium sulfate
0.05 M TRIS pH 8.5
5 % (v/v) Glycerol
0.005 M Magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.16 α = 90 b = 99.16 β = 90 c = 112.18 γ = 120
Symmetry Space Group P 63 2 2
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 16M 2021-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976264 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) 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 2.45 50 100 0.379 0.385 0.998 17.4 37 12518
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.51 3.429 3.4730000000000003 0.792
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.45 49.58 12516 626 99.952 0.209 0.2053 0.2109 0.2743 0.2745 55.996
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] -0.246 -0.123 -0.246 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.959 r_dihedral_angle_4_deg 18.273 r_dihedral_angle_3_deg 18.25 r_lrange_it 11.931 r_lrange_other 11.93 r_scangle_it 9.296 r_scangle_other 9.293 r_dihedral_angle_1_deg 7.907 r_mcangle_it 6.637 r_mcangle_other 6.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.959 r_dihedral_angle_4_deg 18.273 r_dihedral_angle_3_deg 18.25 r_lrange_it 11.931 r_lrange_other 11.93 r_scangle_it 9.296 r_scangle_other 9.293 r_dihedral_angle_1_deg 7.907 r_mcangle_it 6.637 r_mcangle_other 6.634 r_scbond_it 6.405 r_scbond_other 6.402 r_mcbond_it 4.987 r_mcbond_other 4.987 r_angle_refined_deg 1.631 r_angle_other_deg 1.254 r_symmetry_nbd_refined 0.312 r_nbd_other 0.205 r_nbd_refined 0.193 r_symmetry_nbd_other 0.186 r_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.152 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2285 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction PHASER phasing