9RFD | pdb_00009rfd

Human ADP-ribosylhydrolase 3 (ARH3) in complex with ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FOZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	15% (w/v) PEG 4000, 10% (v/v) DMSO, 0.1 M ammonium sulfate, 0.1 M sodium acetate buffer

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.79	α = 116.402
b = 65.76	β = 94.788
c = 69.92	γ = 103.731

Symmetry
Space Group	P 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 4M		2024-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

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	1.85	34.765	96.7	0.105	0.122	0.062	0.995	9.2	3.9		55923			16.2

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	1.85	1.898	84.3		0.523	0.608	0.309	0.816	2.1	3.8

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-Factor (Observed)	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	1.85	34.765	55923	2000	96.691	0.162	0.162	0.1611	0.172	0.1938	0.2025	Random selection	19.324

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]
-0.122	-0.498	-0.405	-0.266	0.307	0.273

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.31
r_dihedral_angle_3_deg	11.584
r_dihedral_angle_2_deg	5.84
r_dihedral_angle_1_deg	5.503
r_lrange_it	4.934
r_lrange_other	4.803
r_scangle_it	3.132
r_scangle_other	3.132
r_mcangle_it	2.203
r_mcangle_other	2.202
r_scbond_it	1.895
r_scbond_other	1.895
r_angle_refined_deg	1.339
r_mcbond_it	1.33
r_mcbond_other	1.33
r_angle_other_deg	0.487
r_symmetry_nbd_refined	0.283
r_nbd_refined	0.218
r_nbtor_refined	0.179
r_symmetry_nbd_other	0.171
r_symmetry_xyhbond_nbd_refined	0.161
r_nbd_other	0.157
r_xyhbond_nbd_refined	0.141
r_symmetry_nbtor_other	0.072
r_chiral_restr	0.071
r_dihedral_angle_other_2_deg	0.008
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	5112
Nucleic Acid Atoms
Solvent Atoms	537
Heterogen Atoms	73

Software

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