4MGE | pdb_00004mge

1.85 Angstrom Resolution Crystal Structure of PTS System Cellobiose-specific Transporter Subunit IIB from Bacillus anthracis.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IIB	PDB ENTRY 1IIB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.3	295	Protein: 7.5 mG/mL, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH 8.3; Screen: Classics II (B7), 0.056 M Sodium phosphate, 1.344 M Potasium phosphate; Cryo: 4.0 M Sodium formate., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.77	30.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.788	α = 90
b = 70.802	β = 90
c = 84.464	γ = 90

Symmetry
Space Group	C 2 2 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	2013-07-25	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)	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	1.85	30	99.6	0.049	33.5	7.1	15627	15627		-3	36.9

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	1.85	1.88	98.1		0.502	3.2	5.9	736

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 1IIB	1.85	29.89	14797	14797	777	99.58	0.17841	0.17841	0.17608	0.19	0.22364	0.23	RANDOM	56.509

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]
-2.93			-0.41		3.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.7
r_dihedral_angle_4_deg	13.66
r_dihedral_angle_3_deg	12.01
r_long_range_B_other	9.159
r_long_range_B_refined	9.149
r_scangle_other	6.167
r_scbond_it	4.242
r_scbond_other	4.223
r_mcangle_it	3.906
r_mcangle_other	3.904
r_dihedral_angle_1_deg	2.971
r_mcbond_it	2.87
r_mcbond_other	2.865
r_angle_refined_deg	1.472
r_angle_other_deg	0.761
r_chiral_restr	0.095
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1616
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	5

Software

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