3SC4 | pdb_00003sc4

Crystal structure of a Short chain dehydrogenase (A0QTM2 homolog) Mycobacterium thermoresistibile

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	290	Internal tracking number 220646H3. Focus screen based on JCSG E2. 2 M ammonium sulfate, 0.1 M cacodylate, pH 6.54, 200 mM sodium chloride. MythA.01365.a.A1 PW28688 at 27.8 mg/mL, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
3.7	67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.49	α = 90
b = 111.49	β = 90
c = 124.88	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	CCD	ADSC QUANTUM 315		2011-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

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	2.5	48.28	99.8	0.101	21.89	9.3	30482	30423		-3	37.017

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	2.5	2.56	100		0.564	4.4	9.2	2240

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 3KVO	2.5	48.28	30393	2343	99.72	0.181	0.178	0.18	0.22	0.22	RANDOM	27.608

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]
-0.45	-0.22		-0.45		0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.398
r_dihedral_angle_4_deg	17.257
r_dihedral_angle_3_deg	14.984
r_dihedral_angle_1_deg	6.567
r_scangle_it	3.052
r_scbond_it	1.837
r_angle_refined_deg	1.46
r_mcangle_it	1.153
r_angle_other_deg	0.906
r_mcbond_it	0.606

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.398
r_dihedral_angle_4_deg	17.257
r_dihedral_angle_3_deg	14.984
r_dihedral_angle_1_deg	6.567
r_scangle_it	3.052
r_scbond_it	1.837
r_angle_refined_deg	1.46
r_mcangle_it	1.153
r_angle_other_deg	0.906
r_mcbond_it	0.606
r_mcbond_other	0.122
r_chiral_restr	0.079
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4113
Nucleic Acid Atoms
Solvent Atoms	150
Heterogen Atoms	30

Software

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