1YHF | pdb_00001yhf

Crystal Structure of Conserved SPY1581 Protein of Unknown Function from Streptococcus pyogenes

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5	293	30% PEG 3000, 0.1 M Sodium Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 4.50

Crystal Properties
Matthews coefficient	Solvent content
2.3	45.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 39.897	α = 90
b = 39.897	β = 90
c = 144.758	γ = 90

Symmetry
Space Group	P 41 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	CCD	SBC-3		2004-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM		APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	40	99.1	0.137	33.6	23.4		8535

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.05	94.8		0.746	2.62	12.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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)	Mean Isotropic B
X-RAY DIFFRACTION	SAD	2	39.9	8492	8492	843	99.3	0.192	0.19	0.1897	0.248	0.2094	31.75

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]
1.42			1.42		-2.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.072
r_dihedral_angle_4_deg	18.461
r_dihedral_angle_3_deg	13.349
r_dihedral_angle_1_deg	6.634
r_scangle_it	3.914
r_scbond_it	2.41
r_angle_refined_deg	1.434
r_mcangle_it	1.229
r_mcbond_it	0.945
r_nbtor_refined	0.304
r_nbd_refined	0.226
r_symmetry_vdw_refined	0.217
r_symmetry_hbond_refined	0.159
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
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	878
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
MLPHARE	phasing
DM	phasing
REFMAC	refinement
HKL-2000	data reduction