8QEU

Crystal structure of ornithine transcarbamylase from Arabidopsis thaliana (AtOTC) in complex with ornithine

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	293	PEG 3350 16%, Lithium sulfate 0.3M, HEPES 0.1M pH 6.0, 20mM ornithine, cryoprotection was obtained by 25% PEG400

Crystal Properties
Matthews coefficient	Solvent content
3.21	61.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.307	α = 90
b = 155.38	β = 90
c = 189.541	γ = 90

Symmetry
Space Group	C 2 2 21

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 PILATUS 6M		2023-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.5	50	99.6	0.072	0.999	17.88	7.33		208445

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59	98.9		0.933	0.731	2.05	7.14

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.5	49.02	207402	1043	99.55	0.11945	0.11927	0.15603	RANDOM	19.788

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]
0.72			-0.21		-0.51

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.2
r_dihedral_angle_2_deg	10.556
r_dihedral_angle_1_deg	6.19
r_long_range_B_refined	4.388
r_rigid_bond_restr	4.273
r_long_range_B_other	3.627
r_scangle_other	2.516
r_mcangle_it	2.174
r_mcangle_other	2.174
r_scbond_other	1.942
r_scbond_it	1.941
r_angle_refined_deg	1.702
r_mcbond_it	1.548
r_mcbond_other	1.548
r_angle_other_deg	0.622
r_chiral_restr	0.097
r_bond_refined_d	0.012
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7189
Nucleic Acid Atoms
Solvent Atoms	1278
Heterogen Atoms	66

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	model building