9XDG | pdb_00009xdg

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

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		293	100mM OAA and 10% volume of a saturated solution of DNTB in 70mM HEPES pH7.0, 7mM MgCl2, 14%(w/v) PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 192.336	α = 90
b = 63.55	β = 90
c = 76.595	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		2022-02-08	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)	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	2.29	43.59	98.96	0.2031	8.96	6.3		42621

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	2.29	2.32			1.375

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	2.294	38.915	42383	1988	98.593	0.207	0.2042	0.2061	0.2658	0.2617	47.723

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]
-2.662			2.754		-0.092

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.399
r_dihedral_angle_6_deg	14.953
r_lrange_other	11.019
r_lrange_it	11.018
r_dihedral_angle_2_deg	10.968
r_scangle_it	7.889
r_scangle_other	7.888
r_dihedral_angle_1_deg	7.177
r_mcangle_it	7.04
r_mcangle_other	7.04
r_scbond_it	5.032
r_scbond_other	5.032
r_mcbond_it	4.603
r_mcbond_other	4.603
r_angle_refined_deg	1.714
r_dihedral_angle_other_3_deg	1.132
r_angle_other_deg	0.559
r_nbd_refined	0.231
r_nbd_other	0.212
r_symmetry_nbd_refined	0.208
r_symmetry_nbd_other	0.202
r_symmetry_xyhbond_nbd_other	0.2
r_xyhbond_nbd_refined	0.191
r_nbtor_refined	0.19
r_symmetry_xyhbond_nbd_refined	0.189
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.077
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6574
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms	73

Software

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