5R50

PanDDA analysis group deposition -- Crystal Structure of human NUDT22 in complex with N13371a

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1M HEPES pH 7.5, 0.3M sodium/potassium phosphate, 15% PEG Smear High, 20% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.673	α = 90
b = 52.376	β = 90
c = 102.019	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 PILATUS 6M		2016-06-23		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92819	Diamond	I04-1

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	1.87	102.02	100	0.093	0.101	0.04	0.998	11.9	6.5		22888

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	1.87	1.97	99.9		0.676	0.732	0.277	0.867		6.8	3266

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	5LF9	1.87	51.01	21584	1251	99.95	0.1823	0.1793	0.233	RANDOM	29.098

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]
2.02			-2.28		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.671
r_dihedral_angle_4_deg	17.022
r_dihedral_angle_3_deg	13.629
r_dihedral_angle_1_deg	6.636
r_mcangle_it	3.086
r_mcbond_it	2.1
r_mcbond_other	2.097
r_angle_refined_deg	1.54
r_angle_other_deg	1.3
r_chiral_restr	0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.671
r_dihedral_angle_4_deg	17.022
r_dihedral_angle_3_deg	13.629
r_dihedral_angle_1_deg	6.636
r_mcangle_it	3.086
r_mcbond_it	2.1
r_mcbond_other	2.097
r_angle_refined_deg	1.54
r_angle_other_deg	1.3
r_chiral_restr	0.077
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2198
Nucleic Acid Atoms
Solvent Atoms	157
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.