5MP0

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5J3T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52770.1 M acetate pH 4.5 25% PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5150.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.05α = 90
b = 60.57β = 90
c = 65.45γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6338.7399.90.08811.36.524476
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.631.6699.71.8950.86.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT5j3t1.6338.7323182124499.740.214410.211870.26178RANDOM30.885
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]
1.94-2.020.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.887
r_dihedral_angle_4_deg16.225
r_dihedral_angle_3_deg12.808
r_long_range_B_other7.075
r_long_range_B_refined7.062
r_dihedral_angle_1_deg6.002
r_scangle_other5.851
r_mcangle_it4.073
r_mcangle_other4.07
r_scbond_it3.998
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.887
r_dihedral_angle_4_deg16.225
r_dihedral_angle_3_deg12.808
r_long_range_B_other7.075
r_long_range_B_refined7.062
r_dihedral_angle_1_deg6.002
r_scangle_other5.851
r_mcangle_it4.073
r_mcangle_other4.07
r_scbond_it3.998
r_scbond_other3.973
r_mcbond_it3.007
r_mcbond_other2.989
r_angle_refined_deg2.028
r_angle_other_deg1.084
r_chiral_restr0.124
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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 AtomsNumber
Protein Atoms1169
Nucleic Acid Atoms
Solvent Atoms60
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing