3R1I | pdb_00003r1i

Crystal structure of a short-chain type dehydrogenase/reductase from Mycobacterium marinum

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	MymaA.01365.b.A1 PS00949 at 55 mg/mL against JCSF+ screen condition D6, 0.2 M MgCl2, 0.1 M Tris pH 8.5, 20% PEG 8000 with 25% ethylene glycol as cryo-protectant, crystal tracking ID 220110d6, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.52	α = 90
b = 127.91	β = 90
c = 105.65	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	2011-03-10	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	99.4	0.06	19.5	5.4	42084	41849		-3	27.831

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	99.4		0.43	3.14	3.2	3084

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	3ctm	1.95	39.24	41760	2105	99.24	0.1655	0.1637	0.17	0.197	0.2	RANDOM	21.951

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]
-0.53			1.38		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.177
r_dihedral_angle_3_deg	11.423
r_dihedral_angle_4_deg	10.836
r_dihedral_angle_1_deg	5.449
r_scangle_it	3.323
r_scbond_it	2.001
r_angle_refined_deg	1.303
r_mcangle_it	1.179
r_mcbond_it	0.675
r_chiral_restr	0.087

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.177
r_dihedral_angle_3_deg	11.423
r_dihedral_angle_4_deg	10.836
r_dihedral_angle_1_deg	5.449
r_scangle_it	3.323
r_scbond_it	2.001
r_angle_refined_deg	1.303
r_mcangle_it	1.179
r_mcbond_it	0.675
r_chiral_restr	0.087
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3645
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	6

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
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.