2BG5 | pdb_00002bg5

Crystal Structure of the Phosphoenolpyruvate-binding Enzyme I-Domain from the Thermoanaerobacter tengcongensis PEP: Sugar Phosphotransferase System (PTS)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1 M SODIUM ACETATE TRIHYDRATE PH 4.6, 12% W/V PEG 4000, 7% V/V MPD

Crystal Properties
Matthews coefficient	Solvent content
2.4	0.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.094	α = 90
b = 91.435	β = 90
c = 181.847	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	110					M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	1.82	40	99.9	0.07	16.5	4		1230055		4.6

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	1.82	1.94	99.7		0.24	4.6

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-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.82	30	120674	2245	99.8	0.209	0.208	0.25	RANDOM	6.47

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]
-1.3			-1		2.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.041
r_dihedral_angle_4_deg	18.255
r_dihedral_angle_3_deg	13.416
r_scangle_it	4.741
r_dihedral_angle_1_deg	4.115
r_scbond_it	3.307
r_mcbond_it	1.907
r_angle_refined_deg	1.876
r_mcangle_it	1.866
r_symmetry_vdw_refined	0.356
r_symmetry_hbond_refined	0.303
r_nbd_refined	0.285
r_xyhbond_nbd_refined	0.207
r_chiral_restr	0.161
r_bond_refined_d	0.015
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10084
Nucleic Acid Atoms
Solvent Atoms	848
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SOLVE	phasing