5Y8O | pdb_00005y8o

Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) + NAD + 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		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
2.83	56.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 129.06	α = 90
b = 129.06	β = 90
c = 70.13	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++		2017-08-10	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	2.05	111.77	99	0.16	6	3.6		41484

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	2.05	2.16	99		0.16	6

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	3OBB	2.05	111.77	39313	2095	98.89	0.17819	0.1757	0.18	0.22508	0.23	RANDOM	23.308

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]
0.11	0.05		0.11		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.452
r_dihedral_angle_4_deg	20.566
r_dihedral_angle_3_deg	14.957
r_long_range_B_refined	7.596
r_long_range_B_other	7.539
r_dihedral_angle_1_deg	6.1
r_scangle_other	3.917
r_scbond_it	2.501
r_scbond_other	2.499
r_mcangle_other	2.331
r_mcangle_it	2.33
r_angle_refined_deg	1.619
r_mcbond_it	1.517
r_mcbond_other	1.479
r_angle_other_deg	1.019
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
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	4097
Nucleic Acid Atoms
Solvent Atoms	518
Heterogen Atoms	87

Software

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