8YKC | pdb_00008ykc

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1C9K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	.2 M ammonium chloride, pH 6.3 and 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.92	α = 90
b = 73.96	β = 90
c = 130.6	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 EIGER X 9M		2024-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 5C (4A)	1	PAL/PLS	5C (4A)

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	1.92	28.212	99.1	0.05	1	34	13		41759

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	1.92	1.97			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	1.921	28.212	41757	2073	99.089	0.223	0.2207	0.2281	0.2714	0.2739	27.318

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]
-0.005			-0.002		0.007

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.276
r_dihedral_angle_4_deg	17.121
r_dihedral_angle_3_deg	15.292
r_dihedral_angle_1_deg	6.923
r_lrange_it	6.325
r_lrange_other	6.302
r_scangle_it	4.528
r_scangle_other	4.491
r_mcangle_it	3.343
r_mcangle_other	3.343
r_scbond_it	2.951
r_scbond_other	2.896
r_mcbond_it	2.262
r_mcbond_other	2.26
r_angle_refined_deg	1.678
r_angle_other_deg	1.311
r_nbd_refined	0.199
r_symmetry_nbd_other	0.188
r_symmetry_xyhbond_nbd_refined	0.186
r_nbd_other	0.161
r_xyhbond_nbd_refined	0.157
r_nbtor_refined	0.15
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.076
r_xyhbond_nbd_other	0.059
r_symmetry_nbd_refined	0.057
r_symmetry_xyhbond_nbd_other	0.022
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3941
Nucleic Acid Atoms
Solvent Atoms	331
Heterogen Atoms	65

Software

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