9ZW5 | pdb_00009zw5

Ubiquitous Bacterial Kinase - UbK1 from Porphyromonas gingivalis

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	6.33	298.15	0.1 M Bis Tris propane pH 6.33, 30% polyethylene glycol 3350, 0.2 M Na/K phosphate, 1.25 mM Beryllium sulphate, 8.75 mM Sodium fluoride and 630 mM Manganese chloride

Crystal Properties
Matthews coefficient	Solvent content
1.71	28.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.856	α = 90
b = 47.788	β = 90
c = 96.997	γ = 90

Symmetry
Space Group	P 21 2 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 PILATUS3 6M		2024-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.18079	CLSI	08B1-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	2.6	42.23	98.8	0.107	0.121	0.055	0.997	9.6	4.2		7011

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.72		99.8	0.67	0.761	0.349	0.879		4.2

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	2.6	42.23	6656	336	98.12	0.19251	0.18922	0.1946	0.25443	0.2424	RANDOM	54.503

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]
1.48			-5.01		3.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.825
r_dihedral_angle_4_deg	17.465
r_dihedral_angle_3_deg	15.337
r_long_range_B_refined	10.868
r_long_range_B_other	10.866
r_scangle_other	7.529
r_mcangle_it	7.198
r_mcangle_other	7.198
r_dihedral_angle_1_deg	6.837
r_scbond_it	4.806
r_scbond_other	4.798
r_mcbond_it	4.67
r_mcbond_other	4.669
r_angle_refined_deg	1.528
r_angle_other_deg	1.246
r_chiral_restr	0.066
r_bond_refined_d	0.007
r_gen_planes_refined	0.006
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	2236
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing