1PVL | pdb_00001pvl

STRUCTURE OF THE PANTON-VALENTINE LEUCOCIDIN F COMPONENT FROM STAPHYLOCOCCUS AUREUS

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.8		pH 6.8

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.74	α = 90
b = 72.38	β = 90
c = 98.93	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	IMAGE PLATE	MARRESEARCH	COLLIMATOR	1997-10-24	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X31	0.8270, 1.1271	EMBL/DESY, HAMBURG	X31

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	24.4	85	0.032	0.06	8	4.6		21089		3	10.9

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)
	2	2.12	88		0.088	0.101	7.2	4.3

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2	24.4	21049	1080	85	0.2012	0.26	0.243	0.29	RANDOM	15.3

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]

RMS Deviations
Key	Refinement Restraint Deviation
p_transverse_tor	27.9
p_staggered_tor	10.9
p_special_tor	5
p_scangle_it	2.656
p_scbond_it	1.688
p_planar_tor	1.4
p_mcangle_it	1.024
p_mcbond_it	0.844
p_xhyhbond_nbd	0.3
p_multtor_nbd	0.242
p_singtor_nbd	0.188
p_xyhbond_nbd	0.163
p_chiral_restr	0.155
p_hb_or_metal_coord	0.05
p_planar_d	0.028
p_angle_d	0.027
p_bond_d	0.012
p_plane_restr	0.0098
p_angle_deg
p_orthonormal_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2401
Nucleic Acid Atoms
Solvent Atoms	168
Heterogen Atoms	24

Software

Software
Software Name	Purpose
SHARP	phasing
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling