9TCB | pdb_00009tcb

Catalytic domain of human PARP15 in complex with BAD

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RY4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	278	20% (w/v) PEG 3350, 0.2 M ammonium chloride No pH buffer in the crystallisation solution; protein stock contained 30 mM Hepes at pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.15	α = 90
b = 68.51	β = 90
c = 159.61	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 EIGER2 X 9M		2024-06-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.96863	ESRF	ID30B

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	1.9	43.483	99.9	0.117	0.122	0.033	0.999	13.7	13.2		39921			28.3

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	1.9	1.949	100		0.882	0.923	0.268	0.838	2.1	11.7

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	1.9	43.483	39921	1849	99.872	0.184	0.1819	0.1907	0.2197	0.2261	Random selection	31.959

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]
-1.914			0.473		1.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	13.781
r_dihedral_angle_2_deg	13.585
r_dihedral_angle_3_deg	11.407
r_lrange_it	7.115
r_lrange_other	7.036
r_dihedral_angle_1_deg	6.694
r_scangle_it	4.78
r_scangle_other	4.779
r_mcangle_other	4.082
r_mcangle_it	4.08
r_scbond_it	3.08
r_scbond_other	3.08
r_mcbond_it	2.598
r_mcbond_other	2.598
r_angle_refined_deg	1.455
r_angle_other_deg	0.51
r_dihedral_angle_other_2_deg	0.364
r_nbd_refined	0.209
r_nbtor_refined	0.189
r_symmetry_nbd_other	0.185
r_xyhbond_nbd_refined	0.151
r_nbd_other	0.146
r_symmetry_xyhbond_nbd_refined	0.14
r_symmetry_nbd_refined	0.117
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.054
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3135
Nucleic Acid Atoms
Solvent Atoms	282
Heterogen Atoms	53

Software

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