9GIA | pdb_00009gia

Crystal Structure of Polyphosphate kinase 2-II (PPK2-II) from Bacillus cereus Apo-form

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	8.5	295	PEG 2000 or 4000 , Tris buffer pH 8.5 and Li2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.134	α = 90
b = 116.815	β = 90
c = 130.54	γ = 90

Symmetry
Space Group	I 2 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 EIGER 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	2.42	48.604	98.6	0.11	0.99	8.6	6.4		26950

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.42	2.52			1.07	0.53

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.55	48.604	23540	1177	99.733	0.213	0.21	0.217	0.273	0.2718	RANDOM	62.603

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]
0.008			-0.035		0.027

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.311
r_dihedral_angle_6_deg	15.048
r_lrange_other	12.896
r_lrange_it	12.893
r_scangle_it	10.716
r_scangle_other	10.66
r_dihedral_angle_2_deg	9.141
r_mcangle_it	8.62
r_mcangle_other	8.619
r_scbond_it	7.249
r_scbond_other	7.156
r_dihedral_angle_1_deg	6.752
r_mcbond_it	6.068
r_mcbond_other	6.068
r_angle_refined_deg	1.678
r_angle_other_deg	0.587
r_nbd_refined	0.226
r_symmetry_nbd_other	0.195
r_symmetry_xyhbond_nbd_refined	0.194
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.148
r_symmetry_nbd_refined	0.144
r_nbd_other	0.131
r_ncsr_local_group_1	0.112
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.007
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	4288
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
AutoProcess	data processing
Coot	model building
PHASER	phasing