8YES | pdb_00008yes

Crystal structure of adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase complexed with adenosylcobinamide-phosphate

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		293	0.15 M Sodium Chloride, 0.1 M Bis-Tris: HCl, pH 6.5, 1.3 M Ammonium Sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.213	α = 90
b = 102.922	β = 90
c = 129.228	γ = 90

Symmetry
Space Group	P 2 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 EIGER X 9M		2023-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	0.97942	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	2.6	47.964	99.9	1	15.4	6.4		41344

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	2.6	2.71			1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.6	47.964	41304	2119	99.761	0.197	0.1931	0.1972	0.2633	0.2645	66.423

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			-0.013		0.015

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.493
r_dihedral_angle_3_deg	19.774
r_dihedral_angle_4_deg	17.102
r_lrange_it	13.676
r_lrange_other	13.675
r_scangle_it	9.386
r_scangle_other	9.37
r_mcangle_it	8.145
r_mcangle_other	8.145
r_dihedral_angle_1_deg	7.824
r_scbond_it	6.396
r_scbond_other	6.366
r_mcbond_it	5.646
r_mcbond_other	5.641
r_angle_refined_deg	2.18
r_angle_other_deg	1.223
r_nbd_other	0.225
r_nbd_refined	0.203
r_symmetry_nbd_other	0.196
r_symmetry_nbd_refined	0.179
r_nbtor_refined	0.153
r_xyhbond_nbd_refined	0.134
r_symmetry_xyhbond_nbd_refined	0.13
r_chiral_restr	0.111
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_symmetry_xyhbond_nbd_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8116
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	610

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing