5ID2 | pdb_00005id2

Asymmetry in the active site of Mycobacterium tuberculosis AhpE upon exposure to Mycothiol

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291	1.8M sodium malonate pH 5.0, 0.1M sodium acetate pH 4.5, 5% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.48	53.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.906	α = 90
b = 146.906	β = 90
c = 33.616	γ = 90

Symmetry
Space Group	P 42

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	ADSC QUANTUM 315	mirrors	2015-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE BL13B1	1.00	NSRRC	BL13B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	2.43	30	99.6	0.067	0.997	14.5	4		27862		3	29.01

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	2.43	2.52	97.3		0.276	2.9	3.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1XXU	2.43	29.94	26336	1387	99.55	0.18777	0.18688	0.19	0.20454	0.21	RANDOM	28.728

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]
0.79			0.79		-1.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.749
r_dihedral_angle_3_deg	12.888
r_dihedral_angle_4_deg	11.776
r_dihedral_angle_1_deg	5.332
r_angle_refined_deg	1.145
r_angle_other_deg	1.021
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.004
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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	4848
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	16

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing