5YH8 | pdb_00005yh8

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

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		289	0.1 M Citric acid pH 3.5, 14% (w/v) Polyethylene glycol 1000

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.782	α = 90
b = 85.474	β = 90
c = 86.315	γ = 90

Symmetry
Space Group	P 2 21 21

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		2017-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NFPSS BEAMLINE BL19U1	0.9785	NFPSS	BL19U1

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	2.12	70.88	99.9	16.1	12.7		30251

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	2.12	70.88	28663	1588	99.77	0.15926	0.15547	0.17	0.22891	0.23	RANDOM	35.342

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]
2.03			-2.13		0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.892
r_dihedral_angle_3_deg	15.946
r_long_range_B_refined	7.485
r_long_range_B_other	7.484
r_dihedral_angle_1_deg	7.135
r_dihedral_angle_4_deg	6.844
r_scangle_other	5.792
r_mcangle_it	3.73
r_mcangle_other	3.73
r_scbond_it	3.696
r_scbond_other	3.696
r_mcbond_it	2.588
r_mcbond_other	2.588
r_angle_refined_deg	1.822
r_angle_other_deg	1.104
r_chiral_restr	0.122
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
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	4064
Nucleic Acid Atoms
Solvent Atoms	325
Heterogen Atoms	92

Software

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