5T0W

Crystal structure of the ancestral amino acid-binding protein AncCDT-1, a precursor of cyclohexadienyl dehydratase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ZV2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	291	A crystal grown in a hanging drop of 2 uL protein (18 mg/mL in 20 mM HEPES pH 7.5, 50 mM NaCl, 1 mM arginine) + 2 uL precipitant (0.2 M lithium sulfate, 0.1 M TRIS pH 8.2, 22% (w/v) PEG 3350) was improved by three rounds of serial microseeding; the crystals were crushed and serially diluted in the precipitant, and new hanging drops were prepared by mixing 2 uL protein and 2 uL microseed suspension.

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.03	α = 90
b = 68.88	β = 90
c = 318.63	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	CCD	ADSC QUANTUM 210r		2015-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX1	0.9501	Australian Synchrotron	MX1

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	2.59	33.66	99.4	0.158	0.993	8.2	6.8		33106			29.2

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	2.59	2.71	99.3		0.775	0.755	2.4	6.9

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4ZV2	2.59	33.19	31387	1686	98.87	0.25518	0.25348	0.28733	RANDOM	43.419

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]
2.35			0.55		-2.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.911
r_dihedral_angle_3_deg	18.623
r_dihedral_angle_4_deg	13.699
r_dihedral_angle_1_deg	6.038
r_long_range_B_refined	3.106
r_long_range_B_other	3.103
r_mcangle_it	1.86
r_mcangle_other	1.859
r_scangle_other	1.5
r_angle_refined_deg	1.372
r_angle_other_deg	1.195
r_mcbond_other	1.046
r_mcbond_it	1.045
r_scbond_it	0.836
r_scbond_other	0.836
r_chiral_restr	0.077
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.006
r_gen_planes_other	0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6937
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	48

Software

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