5MP0

Human m7GpppN-mRNA Hydrolase (DCP2, NUDT20) Catalytic Domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5J3T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	0.1 M acetate pH 4.5 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.51	50.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.05	α = 90
b = 60.57	β = 90
c = 65.45	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		2016-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.9686	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	1.63	38.73	99.9	0.088	11.3	6.5		24476

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.63	1.66	99.7		1.895	0.8	6.5

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5j3t	1.63	38.73	23182	1244	99.74	0.21441	0.21187	0.26178	RANDOM	30.885

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]
1.94			-2.02		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.887
r_dihedral_angle_4_deg	16.225
r_dihedral_angle_3_deg	12.808
r_long_range_B_other	7.075
r_long_range_B_refined	7.062
r_dihedral_angle_1_deg	6.002
r_scangle_other	5.851
r_mcangle_it	4.073
r_mcangle_other	4.07
r_scbond_it	3.998
r_scbond_other	3.973
r_mcbond_it	3.007
r_mcbond_other	2.989
r_angle_refined_deg	2.028
r_angle_other_deg	1.084
r_chiral_restr	0.124
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1169
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms	8

Software

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