8OFO | pdb_00008ofo

Structure of Enterococcus faecium CdaA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2931.5 M Lithium sulfate 0.05 M TRIS pH 8.5 5 % (v/v) Glycerol 0.005 M Magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.4148.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.16α = 90
b = 99.16β = 90
c = 112.18γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2021-09-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)0.976264PETRA III, EMBL c/o DESYP14 (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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.45501000.3790.3850.99817.43712518
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)RedundancyNumber Unique Reflections (All)
12.452.513.4293.47300000000000030.792

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.4549.581251662699.9520.2090.20530.210.27430.2755.996
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]
-0.246-0.123-0.2460.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.959
r_dihedral_angle_4_deg18.273
r_dihedral_angle_3_deg18.25
r_lrange_it11.931
r_lrange_other11.93
r_scangle_it9.296
r_scangle_other9.293
r_dihedral_angle_1_deg7.907
r_mcangle_it6.637
r_mcangle_other6.634
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.959
r_dihedral_angle_4_deg18.273
r_dihedral_angle_3_deg18.25
r_lrange_it11.931
r_lrange_other11.93
r_scangle_it9.296
r_scangle_other9.293
r_dihedral_angle_1_deg7.907
r_mcangle_it6.637
r_mcangle_other6.634
r_scbond_it6.405
r_scbond_other6.402
r_mcbond_it4.987
r_mcbond_other4.987
r_angle_refined_deg1.631
r_angle_other_deg1.254
r_symmetry_nbd_refined0.312
r_nbd_other0.205
r_nbd_refined0.193
r_symmetry_nbd_other0.186
r_xyhbond_nbd_refined0.164
r_nbtor_refined0.152
r_symmetry_xyhbond_nbd_refined0.141
r_chiral_restr0.077
r_symmetry_nbtor_other0.077
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2285
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing