4XGN | pdb_00004xgn

Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from Burkholderia thailandensis

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	Morpheus screen c6: 10% PEG 8000, 20% EG; 30mM each NaNO3, Na2HPO4, (NH4)2SO4; 100mM MOPS/HEPES pH 7.5; ButhA.0010.l.B1.PS01726 at 10mg/ml with 2.5mM NAD; direct cryo; tray 252631c6, puck sxz2-6

Crystal Properties
Matthews coefficient	Solvent content
2.52	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.22	α = 103.26
b = 77.1	β = 93.98
c = 109.35	γ = 109.68

Symmetry
Space Group	P 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	RAYONIX MX-225		2014-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	1.65	50	97.1	0.081	0.094	11.23	4	253404	246070		-3	22.006

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.69	95.4		0.476	0.55	2.88	4

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	3TPC	1.65	50	233814	12256	97.15	0.1557	0.1545	0.17	0.1771	0.19	RANDOM	16.931

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]
0.29	-0.56	0.22	-0.19	-0.01	0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.291
r_dihedral_angle_4_deg	17.08
r_dihedral_angle_3_deg	11.797
r_dihedral_angle_1_deg	5.993
r_angle_refined_deg	1.74
r_mcangle_it	1.107
r_angle_other_deg	0.98
r_mcbond_it	0.634
r_mcbond_other	0.633
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.291
r_dihedral_angle_4_deg	17.08
r_dihedral_angle_3_deg	11.797
r_dihedral_angle_1_deg	5.993
r_angle_refined_deg	1.74
r_mcangle_it	1.107
r_angle_other_deg	0.98
r_mcbond_it	0.634
r_mcbond_other	0.633
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14506
Nucleic Acid Atoms
Solvent Atoms	1923
Heterogen Atoms	468

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
ARP	model building
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

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.