3O8J | pdb_00003o8j

Crystal structure of 2-methylcitrate synthase (PrpC) from Salmonella typhimurium

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1A59	N- (1-12) and C- terminal (361-378) deletion construct of the AbGltA (PDB: 1A59) dimer

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	9	297	0.1M Bicine, 18% PEG 4000, 1.4M ammonium sulfate, 0.2M trisodium citrate , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.068	α = 60.84
b = 118.159	β = 67.77
c = 120.659	γ = 81.92

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	IMAGE PLATE	MAR scanner 345 mm plate	Mirror	2008-07-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	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	2.4	50	90.2	0.092	22.17	1.7		160794			38.2

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)
	2.4	2.49	72.5		0.194	4.18

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	N- (1-12) and C- terminal (361-378) deletion construct of the AbGltA (PDB: 1A59) dimer	2.41	50	159324	137700	7257	91.02	0.22094	0.21762	0.22	0.28247	0.28	RANDOM	40.815

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]
1.71		0.1	-0.05	1.47	-3.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.849
r_dihedral_angle_3_deg	17.784
r_dihedral_angle_4_deg	16.387
r_dihedral_angle_1_deg	5.443
r_scangle_it	1.751
r_angle_refined_deg	1.147
r_scbond_it	1.086
r_mcangle_it	0.762
r_mcbond_it	0.411
r_chiral_restr	0.084

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.849
r_dihedral_angle_3_deg	17.784
r_dihedral_angle_4_deg	16.387
r_dihedral_angle_1_deg	5.443
r_scangle_it	1.751
r_angle_refined_deg	1.147
r_scbond_it	1.086
r_mcangle_it	0.762
r_mcbond_it	0.411
r_chiral_restr	0.084
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	27985
Nucleic Acid Atoms
Solvent Atoms	1178
Heterogen Atoms	66

Software

Software
Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	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.