9IGQ | pdb_00009igq

Crystal structure of PPK2 class III from Erysipelotrichaceae bacterium in complex with AppCH2p and polyphosphate

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	4.6	285	MPD 20%, sodium acetate 0.1 M, sodium chloride 0.2 M

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.888	α = 90
b = 110.734	β = 90
c = 152.585	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 16M		2024-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.976	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.7	48.9	98.4	0.193	0.0533	0.998	10.76	13.7		145127			18.53

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.8	99.8		2.15	0.593	0.635	1.51	12.5

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	1.7	48.9	144529	7180	99.467	0.169	0.1671	0.1671	0.1969	0.197	30.49

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]
-0.228			0.946		-0.717

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.737
r_dihedral_angle_3_deg	13.05
r_lrange_it	8.355
r_lrange_other	8.336
r_scangle_it	6.936
r_scangle_other	6.935
r_dihedral_angle_2_deg	6.688
r_dihedral_angle_1_deg	5.95
r_scbond_it	4.704
r_scbond_other	4.703
r_mcangle_it	3.501
r_mcangle_other	3.501
r_mcbond_it	2.396
r_mcbond_other	2.393
r_angle_refined_deg	2.211
r_dihedral_angle_other_2_deg	1.161
r_angle_other_deg	0.814
r_symmetry_nbd_refined	0.34
r_nbd_other	0.214
r_nbd_refined	0.21
r_nbtor_refined	0.182
r_symmetry_xyhbond_nbd_refined	0.174
r_symmetry_nbd_other	0.155
r_xyhbond_nbd_refined	0.138
r_chiral_restr	0.112
r_ncsr_local_group_5	0.091
r_ncsr_local_group_3	0.086
r_ncsr_local_group_4	0.086
r_ncsr_local_group_2	0.083
r_ncsr_local_group_6	0.077
r_symmetry_nbtor_other	0.073
r_ncsr_local_group_1	0.063
r_bond_refined_d	0.014
r_gen_planes_refined	0.012
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9812
Nucleic Acid Atoms
Solvent Atoms	1008
Heterogen Atoms	330

Software

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