6YVB | pdb_00006yvb

Arabidopsis aspartate transcarbamoylase complex with carbamoyl phosphate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6YS6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		293	Protein at 5 mg/ml in buffer 20 mM Tris pH 7.0, 0.1 M NaCl, 2% glycerol, 0.2 mM tris(2-carboxyethyl) phosphine (TCEP), with 10 mM carbamoyl phosphate. Crystallization solution: 25% PEG3350, 0.2 M Li2SO4 and 0.1 M bis-tris pH 5.5. Cryo-conditions achieved by increasing glycerol concentration up to 20% in presence of carbamoyl phosphate.

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.268	α = 90
b = 109.481	β = 90
c = 212.042	γ = 90

Symmetry
Space Group	P 21 21 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		2019-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97910	ALBA	XALOC

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	1.826	76.278	100	0.051	0.999	17.6	6.7		212623

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	1.826	1.93			1.058	0.704

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6YS6	1.826	76.278	212513	10800	99.906	0.174	0.172	0.18	0.213	0.22	37.606

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]
1.068			-0.039		-1.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.031
r_dihedral_angle_4_deg	18.377
r_dihedral_angle_3_deg	15.809
r_lrange_it	7.509
r_lrange_other	7.482
r_dihedral_angle_1_deg	6.896
r_scangle_it	6.105
r_scangle_other	6.105
r_scbond_it	4.253
r_scbond_other	4.253
r_mcangle_it	4.212
r_mcangle_other	4.212
r_mcbond_it	3.303
r_mcbond_other	3.303
r_angle_refined_deg	1.692
r_angle_other_deg	1.407
r_symmetry_nbd_refined	0.225
r_nbd_refined	0.199
r_nbd_other	0.188
r_symmetry_nbd_other	0.177
r_symmetry_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.162
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.083
r_symmetry_nbtor_other	0.08
r_symmetry_xyhbond_nbd_other	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14733
Nucleic Acid Atoms
Solvent Atoms	1334
Heterogen Atoms	196

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
Aimless	data scaling
PHASER	phasing