6ABX

Crystal structure of citrate synthase (Msed_1522) from Metallosphaera sedula in complex with citrate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1VGP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	295	800mM sodium phosphate monobasic/1200mM potassium phosphate dibasic, 0.1 M sodium acetate/acetic acid pH 4.2

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.181	α = 93.56
b = 53.522	β = 105.73
c = 76.285	γ = 102.16

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	ADSC QUANTUM 270		2017-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	0.97934	PAL/PLS	7A (6B, 6C1)

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	72.84	97.1	0.057	22	3.5		79198

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	1.73			0.263

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VGP	1.7	29.15	75282	3916	96.77	0.1461	0.1443	0.1803	RANDOM	21.068

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]
-0.2	0.89	0.11	0.68	0.43	-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.459
r_dihedral_angle_4_deg	19.468
r_dihedral_angle_3_deg	14.261
r_dihedral_angle_1_deg	5.987
r_angle_refined_deg	1.688
r_angle_other_deg	1.082
r_chiral_restr	0.162
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.459
r_dihedral_angle_4_deg	19.468
r_dihedral_angle_3_deg	14.261
r_dihedral_angle_1_deg	5.987
r_angle_refined_deg	1.688
r_angle_other_deg	1.082
r_chiral_restr	0.162
r_bond_refined_d	0.014
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5918
Nucleic Acid Atoms
Solvent Atoms	593
Heterogen Atoms	44

Software

Software
Software Name	Purpose
HKL-2000	data reduction
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing

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.