5QJ5

PanDDA analysis group deposition -- Crystal Structure of NUDT5 in complex with Z44592329

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	33 % PEG4k, 0.2 MgCl2 and 0.1 M Tris

Crystal Properties
Matthews coefficient	Solvent content
2.41	48.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.146	α = 79.47
b = 59.774	β = 81.89
c = 80.086	γ = 75.78

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 PILATUS 6M		2018-07-07		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	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	1.72	47.4	96.5	0.031	0.044	0.031	0.998	9.7	1.8		88549

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	1.72	1.76	95.6		0.72	1.018	0.72	0.635		1.7	6499

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	6GRU	1.72	78.34	84091	4450	96.4	0.2168	0.2149	0.2534	RANDOM	38.599

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]
3.16	0.94	0.68	-0.6	1.12	-1.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.569
r_dihedral_angle_3_deg	14.516
r_dihedral_angle_4_deg	12.249
r_dihedral_angle_1_deg	7.383
r_mcangle_it	4.429
r_mcbond_other	2.946
r_mcbond_it	2.936
r_angle_refined_deg	1.823
r_angle_other_deg	1.029
r_chiral_restr	0.107
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5723
Nucleic Acid Atoms
Solvent Atoms	249
Heterogen Atoms	81

Software

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