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2.1 Angstrom Crystal Structure of the Complex Between the Nuclear U8 snoRNA Decapping Nudix Hydrolase X29, Manganese and m7G-PPP-A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1U20 PDB ENTRY 1U20
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.68 293 4-5 mg/ml X29, 0.025M HEPES pH 7.68, 3/75% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.27 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.702 α = 90 b = 81.71 β = 90 c = 111.706 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 95 IMAGE PLATE RIGAKU RAXIS IV OSMIC VARIMAX CONFOCAL OPTICS 2005-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 46.17 99.9 0.037 19.8 6.92 27774 57.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.18 100 0.38 4.4 6.88
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1U20 2.1 46.17 27801 27773 2757 99.9 0.217 0.212 0.264 RANDOM 59.1
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.229 r_dihedral_angle_4_deg 16.798 r_dihedral_angle_3_deg 14.288 r_scangle_it 5.896 r_dihedral_angle_1_deg 4.883 r_scbond_it 4.366 r_mcangle_it 2.643 r_mcbond_it 1.799 r_angle_refined_deg 1.137 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.229 r_dihedral_angle_4_deg 16.798 r_dihedral_angle_3_deg 14.288 r_scangle_it 5.896 r_dihedral_angle_1_deg 4.883 r_scbond_it 4.366 r_mcangle_it 2.643 r_mcbond_it 1.799 r_angle_refined_deg 1.137 r_nbtor_refined 0.297 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.118 r_chiral_restr 0.066 r_bond_refined_d 0.014 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 2924 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction CNS refinement CrystalClear data collection CrystalClear data reduction d*TREK data scaling CNS phasing