9IX8

Crystallization and structural characterization of phosphopentomutase from the hyperthermophilic archaeon Thermococcus kodakarensis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q6I7B6-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	20% v/v PEG300, 10% v/v Glycerol, 0.1 M Tris-HCl- pH 8.5, 5% w/v PEG8000

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.772	α = 90
b = 97.575	β = 94
c = 128.15	γ = 90

Symmetry
Space Group	P 1 21 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 EIGER X 4M		2023-11-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.90	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.39	50	98.9	0.125	0.135	0.998	10.48	7		77057

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.39	2.53	97		1.039	0.5	0.7	1.57	6.8

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 (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	2.39	50	74699	2310	99.01	0.2033	0.20111	0.2067	0.27378	0.2707	RANDOM	50.494

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]
0.52		0.53	0.49		-1.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.996
r_dihedral_angle_4_deg	20.915
r_dihedral_angle_3_deg	19.151
r_long_range_B_other	10.838
r_long_range_B_refined	10.833
r_dihedral_angle_1_deg	8.012
r_scangle_other	7.916
r_mcangle_other	6.676
r_mcangle_it	6.675
r_scbond_it	5.222
r_scbond_other	5.221
r_mcbond_it	4.612
r_mcbond_other	4.608
r_angle_refined_deg	1.721
r_angle_other_deg	1.266
r_chiral_restr	0.081
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
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	13803
Nucleic Acid Atoms
Solvent Atoms	419
Heterogen Atoms	48

Software

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