7JJ9

Crystal structure of Zn(II)-bound AdcA from Streptococcus pneumoniae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529110% w/v polyethylene glycol 20000, 18% v/v PEG monomethyl ether 550, 0.03 M CaCl2, 0.03 M MgCl2, 0.1 M MES/imidazole pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.2144.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.109α = 90
b = 44.362β = 106.825
c = 92.627γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2014-07-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX10.954Australian SynchrotronMX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.5819.8499.90.0960.9915.97.46435613.8320172758
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.581.610.8430.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2OSV1.5819.831.3564338320799.90.1660.1640.19821.7
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d17.4983285163
f_angle_d0.948968946658
f_chiral_restr0.0551728816928
f_bond_d0.00915034716041
f_plane_restr0.00678202900481
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3667
Nucleic Acid Atoms
Solvent Atoms645
Heterogen Atoms3

Software

Software
Software NamePurpose
PHENIXrefinement
Aimlessdata reduction
XDSdata scaling
PHASERphasing