5O3U | pdb_00005o3u

Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to Presegetalin F1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		apo PCY1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	PCY1-S562A complex with PresegF1 was crystallized at 13.0 mg/mL with 0.161.3 mM PresegB1 in 27% (w/v) PEG 3350, 100 mM Ca chloride and 0.1 M Bis-Tris at pH 6.5. For cryo protection 10 % (v/v) glycerol were added to reservoir solution.

Crystal Properties
Matthews coefficient	Solvent content
2.17	43.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.86	α = 87.64
b = 85.82	β = 78.32
c = 137.87	γ = 89.52

Symmetry
Space Group	P 1

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 PILATUS3 6M		2016-04-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9785	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.86	73.72	95.8	7.8	3.4		222236

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	apo PCY1	1.86	73.72	222236	11725	95.75	0.19445	0.19295	0.2	0.22338	0.23	RANDOM	27.171

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]
-0.58	0.79	0.63	0.27	-0.75	0.48

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.177
r_dihedral_angle_4_deg	17.865
r_dihedral_angle_3_deg	12.381
r_long_range_B_other	6.682
r_long_range_B_refined	6.678
r_dihedral_angle_1_deg	6.333
r_scangle_other	4.988
r_scbond_it	3.337
r_scbond_other	3.337
r_mcangle_it	2.815
r_mcangle_other	2.815
r_mcbond_it	1.889
r_mcbond_other	1.888
r_angle_refined_deg	1.441
r_angle_other_deg	0.938
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	23233
Nucleic Acid Atoms
Solvent Atoms	930
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing