6YGT | pdb_00006ygt

Crystal structure of variant T52P of the intracellular chorismate mutase from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MPV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293.15	0.2 M Sodium malonate, 0.1 M Bis Tris propane pH=8.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.59	α = 90
b = 59.59	β = 90
c = 46.579	γ = 90

Symmetry
Space Group	P 43 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	100	PIXEL	DECTRIS EIGER X 4M		2018-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.967700	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.635	36.698	88.1	0.075	0.081	0.029	0.995	15.7	8.7		9569

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.635	1.716	33.4		0.445		9.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5MPV	1.635	36.698	9124	445	88.11	0.241	0.2402	0.25	0.2645	0.25	32.922

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]
0.207			0.207		-0.415

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.895
r_dihedral_angle_3_deg	17.68
r_dihedral_angle_4_deg	17.242
r_lrange_it	9.543
r_lrange_other	9.537
r_scangle_it	7.175
r_scangle_other	7.168
r_dihedral_angle_1_deg	5.556
r_scbond_it	4.478
r_scbond_other	4.472
r_mcangle_it	4.274
r_mcangle_other	4.27
r_mcbond_it	3.114
r_mcbond_other	3.074
r_angle_refined_deg	1.711
r_angle_other_deg	1.401
r_symmetry_nbd_refined	0.594
r_symmetry_xyhbond_nbd_refined	0.451
r_nbd_other	0.247
r_xyhbond_nbd_refined	0.241
r_nbd_refined	0.233
r_symmetry_nbd_other	0.194
r_nbtor_refined	0.159
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.078
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	596
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing