9IGR | pdb_00009igr

Crystal structure of PPK2 class III from Erysipelotrichaceae bacterium in complex with 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	5.4	285	MPD 10 %; NaOAc 0.1 M;NaCl 0.2 M; pH 5.40

Crystal Properties
Matthews coefficient	Solvent content
2.98	58.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 160.471	α = 90
b = 88.265	β = 101.151
c = 125.344	γ = 90

Symmetry
Space Group	C 1 2 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 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	2.31	45.11	96.6	0.137	0.0525	0.996	9.03	6.81		72761			50.64

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	2.31	2.45	94.8		17.36	6.53	0.773	0.98	7.06

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	2.311	45.109	72669	3729	96.459	0.178	0.176	0.176	0.2127	0.2129	67.877

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]
-1.021		3.467	0.562		-0.842

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.607
r_dihedral_angle_3_deg	15.553
r_lrange_it	10.683
r_lrange_other	10.609
r_scangle_it	10.083
r_scangle_other	10.025
r_dihedral_angle_2_deg	8.925
r_scbond_it	7.962
r_scbond_other	7.646
r_mcangle_other	7.325
r_mcangle_it	7.322
r_dihedral_angle_1_deg	6.434
r_mcbond_it	5.641
r_mcbond_other	5.641
r_angle_refined_deg	2.747
r_angle_other_deg	0.804
r_symmetry_nbd_refined	0.279
r_nbd_refined	0.236
r_nbd_other	0.21
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.196
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.123
r_symmetry_xyhbond_nbd_refined	0.108
r_ncsr_local_group_5	0.088
r_symmetry_nbtor_other	0.087
r_ncsr_local_group_2	0.086
r_ncsr_local_group_1	0.085
r_ncsr_local_group_6	0.085
r_ncsr_local_group_3	0.082
r_ncsr_local_group_4	0.079
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10038
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	215

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
MxCuBE	data collection
Coot	model building