7P4A | pdb_00007p4a

Non-canonical Staphylococcus aureus pathogenicity island repression.

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	0.4M Ammonium phosphate, 25% PEG200

Crystal Properties
Matthews coefficient	Solvent content
2	39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.211	α = 90
b = 100.211	β = 90
c = 298.688	γ = 120

Symmetry
Space Group	P 61 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 EIGER2 XE 16M		2017-11-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97936	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	2.9	86.76	99.7	0.846	14.2	5.9		20492

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)	Redundancy	Number Unique Reflections (All)
1	2.9	3.08			0.049	0.951	2.4

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.901	83.478	20482	1063	99.432	0.301	0.2985	0.3	0.3428	0.35	RANDOM	94.994

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]
2.692	1.346		2.692		-8.732

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.665
r_lrange_it	16.051
r_lrange_other	16.051
r_dihedral_angle_3_deg	14.708
r_mcangle_it	12.003
r_mcangle_other	12
r_scangle_other	11.06
r_scangle_it	11.059
r_dihedral_angle_4_deg	10.081
r_mcbond_it	7.758
r_mcbond_other	7.758
r_scbond_other	6.853
r_scbond_it	6.852
r_dihedral_angle_1_deg	6.061
r_angle_refined_deg	1.321
r_angle_other_deg	1.199
r_symmetry_xyhbond_nbd_refined	0.246
r_nbd_refined	0.206
r_nbd_other	0.183
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.17
r_symmetry_nbd_refined	0.148
r_xyhbond_nbd_refined	0.123
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.046
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4204
Nucleic Acid Atoms
Solvent Atoms	8
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data scaling
iMOSFLM	data reduction
Coot	model building
CRANK2	phasing