7AKR

Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with ADP-ribose dimer

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	100 mM TrisHCl (pH 8.5), 20% (w/v) PEG4000 and 200 mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.62	α = 90
b = 91.6	β = 105.47
c = 91.09	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 PILATUS3 6M		2019-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96863	Diamond	I24

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	1.95	70.631	99.9	0.145	0.083	0.061	0.996	7.9	6.6		99860

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	1.95	2			1.535	1.665	0.638	0.503	1.3

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6D36	1.95	70.631	99838	4757	99.881	0.188	0.187	0.2106	42.84

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]
0.353		0.917	-1.291		0.374

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.943
r_dihedral_angle_4_deg	19.086
r_dihedral_angle_3_deg	13.152
r_dihedral_angle_1_deg	5.718
r_lrange_it	4.741
r_lrange_other	4.74
r_scangle_it	3.197
r_scangle_other	3.197
r_mcangle_it	2.471
r_mcangle_other	2.471
r_scbond_it	1.934
r_scbond_other	1.934
r_mcbond_it	1.515
r_mcbond_other	1.515
r_angle_refined_deg	1.356
r_angle_other_deg	1.347
r_symmetry_xyhbond_nbd_refined	0.332
r_nbd_other	0.201
r_nbd_refined	0.2
r_symmetry_nbd_refined	0.182
r_symmetry_nbd_other	0.17
r_nbtor_refined	0.157
r_xyhbond_nbd_refined	0.149
r_symmetry_nbtor_other	0.079
r_ncsr_local_group_1	0.074
r_chiral_restr	0.071
r_ncsr_local_group_2	0.066
r_ncsr_local_group_6	0.064
r_ncsr_local_group_5	0.063
r_symmetry_xyhbond_nbd_other	0.061
r_ncsr_local_group_3	0.059
r_ncsr_local_group_4	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10351
Nucleic Acid Atoms
Solvent Atoms	437
Heterogen Atoms	327

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing