5YHG | pdb_00005yhg

The crystal structure of Staphylococcus aureus CntA in complex with staphylopine and zinc

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		287	0.1M BICINE pH 8.5, 8%(w/v) Polyethylene glycol monomethyl ether 5000

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.07	α = 90
b = 156.349	β = 90
c = 42.257	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	77	PIXEL	DECTRIS PILATUS3 6M		2017-03-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.9778	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.03	78.3	99.7	24.9	12.1		37675

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 (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	THROUGHOUT	2.03	78.3	35917	1886	99.44	0.16175	0.15908	0.17	0.21312	0.22	RANDOM	45.641

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]
2.93			-4.78		1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.345
r_dihedral_angle_3_deg	15.178
r_dihedral_angle_4_deg	10.562
r_long_range_B_other	8.12
r_long_range_B_refined	8.116
r_scangle_other	6.918
r_dihedral_angle_1_deg	6.662
r_scbond_it	4.807
r_scbond_other	4.806
r_mcangle_it	4.35
r_mcangle_other	4.349
r_mcbond_it	3.409
r_mcbond_other	3.402
r_angle_refined_deg	1.906
r_angle_other_deg	1.093
r_chiral_restr	0.124
r_bond_refined_d	0.018
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4039
Nucleic Acid Atoms
Solvent Atoms	344
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing