4JGA | pdb_00004jga

X-ray crystal structure of 3-oxoacyl-[acyl-carrier-protein] synthase 2 from Rickettsia rickettsii

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	289	JCSG+ A10: 200 mM potassium formate, 20% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.17	α = 90
b = 62.74	β = 112.08
c = 95.43	γ = 90

Symmetry
Space Group	P 1 21 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+		2013-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54

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	2.1	50	98.9	0.104	19.6		47095	46577		-3	19.917

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	2.1	2.15	92		0.298	5.86

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 (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 3KZU	2.1	19.19	47095	46576	2355	99.01	0.1494	0.1479	0.16	0.178	0.19	RANDOM	15.695

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]
0.01		0.14	0.26		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.026
r_dihedral_angle_4_deg	16.295
r_dihedral_angle_3_deg	12.598
r_dihedral_angle_1_deg	5.902
r_angle_refined_deg	1.421
r_angle_other_deg	0.98
r_mcangle_it	0.646
r_mcbond_it	0.367
r_mcbond_other	0.367
r_chiral_restr	0.079

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.026
r_dihedral_angle_4_deg	16.295
r_dihedral_angle_3_deg	12.598
r_dihedral_angle_1_deg	5.902
r_angle_refined_deg	1.421
r_angle_other_deg	0.98
r_mcangle_it	0.646
r_mcbond_it	0.367
r_mcbond_other	0.367
r_chiral_restr	0.079
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6205
Nucleic Acid Atoms
Solvent Atoms	601
Heterogen Atoms	7

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
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.