4JV3 | pdb_00004jv3

Crystal structure of beta-ketoacyl synthase from Brucella melitensis in complex with platencin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LRF	pdb entry 3LRF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	290	MD PACT screen, H2: 20% PEG 3350, 100mM BisTrisPropane pH 8.5, 200mM Na-bromide; tray 233841 f11, BrabA.00113.a at 23 mg/ml, 2.5mM platencin, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.16	α = 90
b = 84.48	β = 120.81
c = 74.02	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	RIGAKU SATURN 944+	Rigaku VariMax	2013-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	1.7	50	98.5	0.033	47.79	11.2	45545	44869		-3	20.929

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	1.7	1.74	96.8		0.187	7.52

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 3LRF	1.7	42.28	45545	44869	2264	98.79	0.14382	0.1438	0.1425	0.16	0.1689	0.18	RANDOM	16.929

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]
-0.06		0.35	-0.1		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.503
r_dihedral_angle_4_deg	16.402
r_dihedral_angle_3_deg	12.637
r_dihedral_angle_1_deg	6.471
r_angle_refined_deg	1.354
r_mcangle_it	1.19
r_angle_other_deg	0.766
r_mcbond_it	0.736
r_mcbond_other	0.734
r_chiral_restr	0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.503
r_dihedral_angle_4_deg	16.402
r_dihedral_angle_3_deg	12.637
r_dihedral_angle_1_deg	6.471
r_angle_refined_deg	1.354
r_mcangle_it	1.19
r_angle_other_deg	0.766
r_mcbond_it	0.736
r_mcbond_other	0.734
r_chiral_restr	0.09
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3005
Nucleic Acid Atoms
Solvent Atoms	433
Heterogen Atoms	31

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
JDirector	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.