2QK7 | pdb_00002qk7

A covalent S-F heterodimer of staphylococcal gamma-hemolysin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LKF	pdb entries 1LKF, 1T5R
experimental model	PDB	1T5R	pdb entries 1LKF, 1T5R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	285	covalent complex concentrated to 9 mg/ml in 50 mM MES-NaOH, 50 mM NaCl, pH 6.5. Needle and rod shape like crystals obtained in drops prepared by mixing two volumes of protein and one volume of reservoir solution containing 10% polyethylene glycol 8000, 0.05 M Na citrate, pH 5.5. Reservoir volumes of 500 mul used, VAPOR DIFFUSION, SITTING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
3.06	59.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 140	α = 90
b = 140	β = 90
c = 73.078	γ = 120

Symmetry
Space Group	P 61

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100				2005-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.9330	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	50.5	100	0.078	8	7	32122	32122

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	100		0.318	2.3	6.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	pdb entries 1LKF, 1T5R	2.4	30	30458	1625	100	0.1825	0.17953	0.18	0.2388	0.24	RANDOM	46.121

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]
0.4	0.2		0.4		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.239
r_dihedral_angle_3_deg	17.366
r_dihedral_angle_4_deg	17.234
r_dihedral_angle_1_deg	7.849
r_scangle_it	4.861
r_scbond_it	3.301
r_mcangle_it	2.153
r_angle_refined_deg	2.028
r_mcbond_it	1.257
r_nbtor_refined	0.318
r_nbd_refined	0.225
r_symmetry_vdw_refined	0.172
r_xyhbond_nbd_refined	0.154
r_chiral_restr	0.135
r_symmetry_hbond_refined	0.135
r_bond_refined_d	0.024
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4303
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
PHASER	phasing