3PGX | pdb_00003pgx

Crystal structure of a putative carveol dehydrogenase from Mycobacterium paratuberculosis bound to nicotinamide adenine dinucleotide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OEC	PDB ENTRY 3oec

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	289	protein at 23.8 mg/mL in 20 mM Hepes pH 7, 300 mM NaCl, 5% glycerol, DTT, 0.2 M MgCl2, 0.1 M Bis Tris, 25% PEG 3350 with 25% ethylene glycol as cryo-protectant, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.03	α = 90
b = 57.92	β = 91.35
c = 131.74	γ = 90

Symmetry
Space Group	C 1 2 1

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 315r		2010-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.97946	ALS	5.0.3

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	1.85	50	97.9	0.093	14.15	4.6	84005	82274		-3	21.352

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	1.85	1.9	97		0.471	3.6	4.7	6159

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	PDB ENTRY 3oec	1.85	50	82151	4114	97.8	0.1471	0.1446	0.15	0.1949	0.2	RANDOM	15.0129

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]
0.97		0.11	-0.56		-0.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.862
r_dihedral_angle_4_deg	16.07
r_dihedral_angle_3_deg	11.349
r_dihedral_angle_1_deg	5.787
r_scangle_it	3.14
r_scbond_it	2.039
r_angle_refined_deg	1.484
r_mcangle_it	1.189
r_mcbond_it	0.719
r_chiral_restr	0.1

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.862
r_dihedral_angle_4_deg	16.07
r_dihedral_angle_3_deg	11.349
r_dihedral_angle_1_deg	5.787
r_scangle_it	3.14
r_scbond_it	2.039
r_angle_refined_deg	1.484
r_mcangle_it	1.189
r_mcbond_it	0.719
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7942
Nucleic Acid Atoms
Solvent Atoms	969
Heterogen Atoms	176

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.