9GP9 | pdb_00009gp9

Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Lysinibacillus fusiformis bound to ADP (form I)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CZP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	295	Ammonium Sulfate and MES pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 109.782	α = 90
b = 109.782	β = 90
c = 286.68	γ = 90

Symmetry
Space Group	I 41 2 2

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 EIGER2 X 16M	Two-stage focusing X-ray optics	2020-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0	SLS	X06SA

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	2.88	48.39	99	0.089	0.99	16.4	8.9		20089

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.88	3.03			1.5

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	2.88	48.39	20089	1005	98.562	0.192	0.1895	0.1961	0.2437	0.2386	92.621

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]
-0.013			-0.013		0.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.53
r_lrange_it	19.881
r_lrange_other	19.881
r_dihedral_angle_2_deg	19.361
r_scangle_it	16.711
r_scangle_other	16.598
r_dihedral_angle_6_deg	14.144
r_mcangle_other	12.865
r_mcangle_it	12.86
r_scbond_it	12.212
r_scbond_other	12.065
r_mcbond_it	9.747
r_mcbond_other	9.738
r_dihedral_angle_1_deg	6.268
r_angle_refined_deg	1.79
r_dihedral_angle_other_2_deg	0.592
r_angle_other_deg	0.589
r_symmetry_xyhbond_nbd_refined	0.301
r_symmetry_nbd_refined	0.26
r_nbd_refined	0.237
r_nbd_other	0.21
r_symmetry_nbd_other	0.199
r_nbtor_refined	0.194
r_xyhbond_nbd_refined	0.153
r_ncsr_local_group_1	0.109
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.079
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	3341
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	84

Software

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