9X0I | pdb_00009x0i

Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4G6B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	20mM CoA and 20mM OAA in 90mM HEPES pH7.0, 9mM MgCl2, 18%(w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 193.859	α = 90
b = 60.597	β = 90
c = 76.864	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	PIXEL	DECTRIS EIGER X 16M		2019-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	38.32	98.6	0.999	17.1	6.7		100323

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.74			0.926

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.7	38.32	99058	1977	98.63	0.159	0.1659	0.172	0.1967	0.2059	29.84

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]
-1.547			0.791		0.757

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.31
r_dihedral_angle_3_deg	12.989
r_lrange_it	7.531
r_lrange_other	7.531
r_dihedral_angle_1_deg	6.135
r_scangle_it	5.981
r_scangle_other	5.98
r_dihedral_angle_2_deg	5.342
r_mcangle_other	3.974
r_scbond_it	3.974
r_mcangle_it	3.973
r_scbond_other	3.945
r_mcbond_it	2.805
r_mcbond_other	2.801
r_angle_refined_deg	1.88
r_angle_other_deg	0.642
r_nbd_refined	0.225
r_symmetry_xyhbond_nbd_refined	0.206
r_nbd_other	0.191
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.184
r_symmetry_nbd_refined	0.179
r_metal_ion_refined	0.139
r_chiral_restr	0.096
r_symmetry_nbtor_other	0.078
r_dihedral_angle_other_2_deg	0.065
r_bond_refined_d	0.011
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	6892
Nucleic Acid Atoms
Solvent Atoms	787
Heterogen Atoms	152

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing