3BJV | pdb_00003bjv

The Crystal Structure of a putative PTS IIA(PtxA) from Streptococcus mutans

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7.9	289	0.1M Tris-Hcl, 1.9-2.1M (NH4)2SO4, pH 7.9, Vapor diffusion, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.754	α = 90
b = 40.754	β = 90
c = 169.556	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	CCD	BRUKER SMART 6000		2007-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR-H	1.5418

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	2.4	40.65	97.1	0.0717	0.0717	10.08	9.3	6206	6026			32

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	2.4	2.54	85.1		0.1297	0.1297	0.1297	9	897

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	PDB ENTRY 2OQT	2.4	27.28	6170	5982	835	96.95	0.191	0.166	0.154	0.1517	0.241	0.2421	RANDOM	15.719

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]
0.24			0.24		-0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.462
r_dihedral_angle_3_deg	18.385
r_dihedral_angle_4_deg	14.65
r_dihedral_angle_1_deg	6.39
r_scangle_it	5.313
r_scbond_it	3.08
r_angle_refined_deg	1.826
r_mcangle_it	1.773
r_mcbond_it	1.135
r_nbtor_refined	0.31
r_symmetry_vdw_refined	0.256
r_nbd_refined	0.22
r_xyhbond_nbd_refined	0.181
r_chiral_restr	0.133
r_symmetry_hbond_refined	0.106
r_bond_refined_d	0.02
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1203
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data collection
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling