4RH6 | pdb_00004rh6

2.9 Angstrom Crystal Structure of Putative Exotoxin 3 from Staphylococcus aureus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RDH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Protein: 8.0 mg/ml, 0.5 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3); Screen: PEGs (C10), 0.1M MES (pH 6.5), 25% (w/v) PEG 8000., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.427	α = 90
b = 90.623	β = 90
c = 159.711	γ = 90

Symmetry
Space Group	P 21 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	100	CCD	MARMOSAIC 300 mm CCD	Beryllium lenses	2014-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (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	2.9	30	95.4	0.121	0.121	10.4	4.2	13668	13668		-3	58.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	2.95	100		0.5	0.5	2.7	4.3	714

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2RDH	2.9	29.96	12253	12253	1372	95.01	0.23143	0.23143	0.22562	0.22	0.28252	0.28	RANDOM	54.042

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]
-3.76			-1.67		5.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.031
r_dihedral_angle_4_deg	12.522
r_dihedral_angle_3_deg	11.672
r_long_range_B_refined	6.897
r_long_range_B_other	6.875
r_mcangle_it	4.152
r_mcangle_other	4.152
r_scangle_other	4.123
r_mcbond_it	2.52
r_mcbond_other	2.519
r_scbond_it	2.445
r_scbond_other	2.418
r_dihedral_angle_1_deg	2.078
r_angle_refined_deg	1.538
r_angle_other_deg	1.03
r_chiral_restr	0.09
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4588
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	3

Software

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