4X9K | pdb_00004x9k

Beta-ketoacyl-acyl carrier protein synthase III-2 (FabH2)(C113A) from Vibrio cholerae

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4WZU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	289	0.2M Sodium malonate pH 7.0,20% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.459	α = 90
b = 61.521	β = 90
c = 69.676	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARMOSAIC 300 mm CCD	Beyllium Lenses	2013-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9786	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.61	50	98.3	0.068	0.075	0.032	11.4	5		47520

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.64	87.3		0.376	0.43	0.205	0.905		4	2077

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	4WZU	1.61	50	45088	2408	98.96	0.153	0.1517	0.17	0.1763	0.19	RANDOM	17.768

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]
-0.73			0.53		0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.12
r_dihedral_angle_4_deg	17.519
r_dihedral_angle_3_deg	11.288
r_dihedral_angle_1_deg	6.331
r_mcangle_it	1.398
r_angle_refined_deg	1.311
r_mcbond_it	0.887
r_mcbond_other	0.886
r_angle_other_deg	0.79
r_chiral_restr	0.083

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.12
r_dihedral_angle_4_deg	17.519
r_dihedral_angle_3_deg	11.288
r_dihedral_angle_1_deg	6.331
r_mcangle_it	1.398
r_angle_refined_deg	1.311
r_mcbond_it	0.887
r_mcbond_other	0.886
r_angle_other_deg	0.79
r_chiral_restr	0.083
r_bond_refined_d	0.008
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	2685
Nucleic Acid Atoms
Solvent Atoms	424
Heterogen Atoms	14

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction
HKL-3000	data scaling

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.