8YEP | pdb_00008yep

Crystal structure of adenosylcobinamide kinase / adenosylcobinamide phosphate guanylyltransferase from Methylocapsa palsarum

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	0.09 M NPS (sodium nitrate, sodium phosphate dibasic, ammonium sulfate), 0.1 M Buffer System 3 (Tris, Bicine (pH 8.5)), and 37.5% of Precipitant Mix 4 (25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350)

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.6	α = 90
b = 104.97	β = 90
c = 111.5	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		2022-11-24	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	1.8	29.654	99.8	0.05	1	26.1	13.3		57890

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	1.8	1.84			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	1.8	29.654	57890	2794	99.709	0.223	0.2218	0.2266	0.2565	0.2631	41.419

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]
-0.002			0.003		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.377
r_dihedral_angle_4_deg	18.504
r_dihedral_angle_3_deg	15.175
r_lrange_other	7.984
r_lrange_it	7.975
r_dihedral_angle_1_deg	7.163
r_scangle_other	6.314
r_scangle_it	6.31
r_mcangle_it	4.885
r_mcangle_other	4.885
r_scbond_it	4.294
r_scbond_other	4.291
r_mcbond_it	3.491
r_mcbond_other	3.491
r_angle_refined_deg	1.555
r_angle_other_deg	1.308
r_xyhbond_nbd_other	0.214
r_nbd_other	0.212
r_nbd_refined	0.202
r_symmetry_nbd_other	0.192
r_symmetry_xyhbond_nbd_refined	0.187
r_symmetry_nbd_refined	0.168
r_nbtor_refined	0.153
r_xyhbond_nbd_refined	0.142
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.075
r_symmetry_xyhbond_nbd_other	0.014
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	3721
Nucleic Acid Atoms
Solvent Atoms	127
Heterogen Atoms	15

Software

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