8X5J | pdb_00008x5j

The Crystal Structure of PARP5A from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DVI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1M Ammonium Tartrate, 16% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.674	α = 90
b = 52.179	β = 93.842
c = 68.089	γ = 90

Symmetry
Space Group	P 1 21 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 9M		2023-02-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.95373	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	48.082	98.3	0.082	10.8	4.8		48348

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	1.7	1.73			0.69

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	48.082	48329	2553	98.05	0.19	0.1888	0.2	0.2084	0.22	25.156

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]
0.277		1.13	0.071		-0.496

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.274
r_dihedral_angle_3_deg	12.87
r_dihedral_angle_4_deg	10.801
r_dihedral_angle_1_deg	6.754
r_lrange_it	6.214
r_lrange_other	6.112
r_scangle_it	3.47
r_scangle_other	3.469
r_mcangle_it	3.009
r_mcangle_other	3.008
r_scbond_it	2.113
r_scbond_other	2.113
r_mcbond_other	1.834
r_mcbond_it	1.833
r_angle_refined_deg	1.373
r_angle_other_deg	1.302
r_nbd_other	0.242
r_nbd_refined	0.199
r_symmetry_nbd_refined	0.183
r_symmetry_nbd_other	0.178
r_symmetry_xyhbond_nbd_refined	0.165
r_nbtor_refined	0.164
r_xyhbond_nbd_refined	0.148
r_ncsr_local_group_1	0.103
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.063
r_bond_refined_d	0.007
r_gen_planes_refined	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	3357
Nucleic Acid Atoms
Solvent Atoms	425
Heterogen Atoms	36

Software

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