8BAU | pdb_00008bau

Phytophthora nicotianae var. parasitica NADAR in complex with ADP-ribose

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	7.5	294	0.1 M Sodium HEPES pH 7.5, 20% (w/v) PEG10000

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.829	α = 90
b = 66.593	β = 90
c = 72.888	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 XE 16M		2022-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97629	Diamond	I03

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	1.6	49.212	100	0.072	0.077	0.024	1	13	9.6		29538

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	1.6	1.63			2.128	2.246	0.712	0.596	0.9	9.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	AlphaFold	1.6	49.212	29479	1425	99.959	0.199	0.1976	0.21	0.2279	0.24	31.797

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]
-1.493			-1.001		2.494

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.364
r_dihedral_angle_3_deg	14.097
r_dihedral_angle_2_deg	9.578
r_lrange_it	7.173
r_lrange_other	7.169
r_scangle_it	6.082
r_scangle_other	6.079
r_dihedral_angle_1_deg	5.939
r_scbond_it	4.325
r_scbond_other	4.323
r_mcangle_it	3.343
r_mcangle_other	3.341
r_mcbond_it	2.744
r_mcbond_other	2.744
r_angle_refined_deg	1.907
r_angle_other_deg	0.653
r_symmetry_nbd_refined	0.245
r_nbd_other	0.229
r_nbd_refined	0.223
r_nbtor_refined	0.191
r_symmetry_nbd_other	0.185
r_symmetry_xyhbond_nbd_refined	0.128
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.094
r_symmetry_nbtor_other	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1536
Nucleic Acid Atoms
Solvent Atoms	88
Heterogen Atoms	56

Software

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