8JSZ | pdb_00008jsz

Crystal structure of a uridylate cyclase from Anabaena sp.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1 M BIS-TRIS pH 6.5, 0.2 M Magnesium chloride hexahydrate, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.661	α = 71.21
b = 50.792	β = 83.96
c = 71.391	γ = 62.07

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 EIGER2 X 16M		2022-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 07A	0.97626	NSRRC	TPS 07A

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	1.83	30	97.6	0.998	27.5	5.5		47377

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	1.84	1.91	95.1		0.972		5.3

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	AlphaFold	1.83	25.05	25040	22277	96.57	0.17765	0.17651	0.1779	0.17893	0.1813	RANDOM	21.504

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]
-0.08	0.16	0.09	-0.24	-0.26	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.829
r_dihedral_angle_4_deg	19.667
r_dihedral_angle_3_deg	13.744
r_long_range_B_other	8.982
r_long_range_B_refined	8.962
r_scangle_other	8.101
r_scbond_it	6.351
r_scbond_other	6.349
r_dihedral_angle_1_deg	6.171
r_mcangle_it	5.986
r_mcangle_other	5.986
r_mcbond_it	4.749
r_mcbond_other	4.699
r_angle_other_deg	2.225
r_angle_refined_deg	1.731
r_chiral_restr	0.097
r_bond_other_d	0.034
r_bond_refined_d	0.014
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
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	4168
Nucleic Acid Atoms
Solvent Atoms	648
Heterogen Atoms	24

Software

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