2A8T

2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 snoRNA Decapping Nudix Hydrolase X29, Manganese and m7G-PPP-A


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U20PDB ENTRY 1U20

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.682934-5 mg/ml X29, 0.025M HEPES pH 7.68, 3/75% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2745.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.702α = 90
b = 81.71β = 90
c = 111.706γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95IMAGE PLATERIGAKU RAXIS IVOSMIC VARIMAX CONFOCAL OPTICS2005-04-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.146.1799.90.03719.86.922777457.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.181000.384.46.88

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1U202.146.172780127773275799.90.2170.2120.264RANDOM59.1
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]
3.62-0.66-2.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.229
r_dihedral_angle_4_deg16.798
r_dihedral_angle_3_deg14.288
r_scangle_it5.896
r_dihedral_angle_1_deg4.883
r_scbond_it4.366
r_mcangle_it2.643
r_mcbond_it1.799
r_angle_refined_deg1.137
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.229
r_dihedral_angle_4_deg16.798
r_dihedral_angle_3_deg14.288
r_scangle_it5.896
r_dihedral_angle_1_deg4.883
r_scbond_it4.366
r_mcangle_it2.643
r_mcbond_it1.799
r_angle_refined_deg1.137
r_nbtor_refined0.297
r_nbd_refined0.198
r_symmetry_vdw_refined0.16
r_xyhbond_nbd_refined0.128
r_symmetry_hbond_refined0.118
r_chiral_restr0.066
r_bond_refined_d0.014
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2924
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms108

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
CNSrefinement
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing