4RGB | pdb_00004rgb

Crystal structure of a putative carveol dehydrogenase from Mycobacterium avium bound to NAD

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	MyavA.01326.g.A1 PS01550 at 20 mg/mL with 2.5 mM NAD against MCSG1 condition C12, 0.1 M BisTrisHCL pH 6.5, 25% PEG 3350 supplemented with 15% EG as cryo-protectant, crystal tracking ID 257485c12, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.53	α = 90
b = 106.37	β = 90
c = 135.87	γ = 90

Symmetry
Space Group	C 2 2 21

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	RIGAKU SATURN 944+	VariMax	2014-09-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	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	1.95	50	98.3	0.052	21.84	5.8	43895	43134		-3	32.389

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	1.95	2	92		0.382	2.75

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	3TSC	1.95	50	40966	2168	98.26	0.2082	0.2065	0.22	0.2411	0.26	RANDOM	40.776

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]
1.71			-1.75		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.047
r_dihedral_angle_4_deg	20.678
r_dihedral_angle_3_deg	13.531
r_dihedral_angle_1_deg	6.175
r_angle_refined_deg	1.441
r_mcangle_it	1.322
r_angle_other_deg	0.93
r_mcbond_it	0.777
r_mcbond_other	0.772
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.047
r_dihedral_angle_4_deg	20.678
r_dihedral_angle_3_deg	13.531
r_dihedral_angle_1_deg	6.175
r_angle_refined_deg	1.441
r_mcangle_it	1.322
r_angle_other_deg	0.93
r_mcbond_it	0.777
r_mcbond_other	0.772
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4019
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	88

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.