5Y8P

Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + 3-Hydroxy propionate (3-HP)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OBB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	295	0.02M MgCl2.6H2O, 0.1M HEPES pH 7.5, 22% w/v polyacrylic acid sodium salt 5100

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 128.92	α = 90
b = 128.92	β = 90
c = 70.19	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2015-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	2.15	111.65	92.5	0.2	7.4	8.3		33570

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	2.15	2.27	92.5		0.223	7.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3OBB	2.15	111.65	31857	1679	92.37	0.16936	0.16688	0.2158	RANDOM	19.377

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]
0.22	0.11		0.22		-0.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.18
r_dihedral_angle_4_deg	19.745
r_dihedral_angle_3_deg	14.248
r_dihedral_angle_1_deg	6.364
r_long_range_B_refined	5.721
r_long_range_B_other	5.592
r_scangle_other	3.11
r_mcangle_other	2.045
r_mcangle_it	2.044
r_scbond_it	1.993
r_scbond_other	1.988
r_angle_refined_deg	1.732
r_mcbond_it	1.271
r_mcbond_other	1.27
r_angle_other_deg	1.083
r_chiral_restr	0.111
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4093
Nucleic Acid Atoms
Solvent Atoms	473
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing