7AKS

Human ADP-ribosylserine hydrolase ARH3 mutant E41A in complex with H2B-S7-mar peptide

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	sodium citrate (pH 6.1), 18% (w/v) PEG4000 and 400 mM ammonium acetate

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.36	α = 90
b = 158.638	β = 90
c = 74.92	γ = 90

Symmetry
Space Group	P 21 21 2

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		2019-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.968630	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	1.86	158.62	99.9	0.167	0.171	0.036	0.999	12.9	21.4		124986

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	1.86	1.9	97.7		1.824	1.905	0.532	0.542	1.4	11.5

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	1.86	97.572	124986	6145	99.205	0.17	0.1685	0.1946	29.039

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]
1.194			0.37		-1.564

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.599
r_dihedral_angle_4_deg	19.571
r_dihedral_angle_3_deg	13.323
r_lrange_it	6.059
r_lrange_other	6.054
r_dihedral_angle_1_deg	5.639
r_scangle_it	3.692
r_scangle_other	3.692
r_mcangle_it	2.662
r_mcangle_other	2.662
r_scbond_it	2.288
r_scbond_other	2.288
r_mcbond_it	1.687
r_mcbond_other	1.683
r_angle_refined_deg	1.56
r_angle_other_deg	1.464
r_symmetry_nbd_refined	0.268
r_nbd_other	0.227
r_nbd_refined	0.226
r_symmetry_nbd_other	0.18
r_xyhbond_nbd_refined	0.17
r_nbtor_refined	0.166
r_symmetry_xyhbond_nbd_refined	0.109
r_symmetry_xyhbond_nbd_other	0.102
r_ncsr_local_group_6	0.094
r_ncsr_local_group_1	0.093
r_ncsr_local_group_5	0.091
r_ncsr_local_group_2	0.089
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_4	0.074
r_ncsr_local_group_3	0.067
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10274
Nucleic Acid Atoms
Solvent Atoms	758
Heterogen Atoms	377

Software

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