7XJT

Catabolic ornithine carbamoyltransferases (OTCs) from Psychrobacter sp. PAMC 21119

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1M Tris-HCl pH 8.1, 1.3M Lithium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
3.61	65.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.061	α = 90
b = 130.061	β = 90
c = 329.326	γ = 120

Symmetry
Space Group	H 3

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 9M		2021-04-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.9794	PAL/PLS	5C (4A)

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	2.598	46.527	99.9	0.995	31.3	5.3		63985			65.96

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	2.598	2.65			0.959

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	modeled	2.598	46.527	63884	3460	99.674	0.205	0.2013	0.2642	79.593

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]
-0.002	-0.001		-0.002		0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.163
r_dihedral_angle_3_deg	19.466
r_dihedral_angle_4_deg	18.169
r_lrange_it	16.46
r_lrange_other	16.46
r_mcangle_it	12.019
r_mcangle_other	12.019
r_scangle_it	11.783
r_scangle_other	11.772
r_mcbond_it	8.213
r_mcbond_other	8.204
r_dihedral_angle_1_deg	8.153
r_scbond_it	7.883
r_scbond_other	7.876
r_angle_refined_deg	1.721
r_angle_other_deg	1.26
r_nbd_refined	0.222
r_symmetry_nbd_other	0.198
r_nbd_other	0.19
r_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.17
r_symmetry_xyhbond_nbd_refined	0.164
r_symmetry_nbd_refined	0.141
r_symmetry_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.073
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10383
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms	5

Software

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