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2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-methyl-GTP
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 VAPOR DIFFUSION, SITTING DROP 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 = 50.2 α = 90 b = 82.15 β = 90 c = 112.24 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 IMAGE PLATE RIGAKU RAXIS IIC Osmic Confocal Optics 2004-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.45 23.51 99.4 0.046 14.1 3.46 17716 17613
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 2.45 2.54 99.5 0.365 3.1 3.48 1727
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1U20 2.45 23 17716 17559 1739 99.38 0.227 0.222 0.2308 0.263 RANDOM 63.01
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] 4.24 -0.97 -3.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.647 r_dihedral_angle_4_deg 18.663 r_dihedral_angle_3_deg 15.002 r_scangle_it 6.457 r_dihedral_angle_1_deg 5.396 r_scbond_it 5.082 r_mcangle_it 2.909 r_mcbond_it 1.969 r_angle_refined_deg 1.222 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.647 r_dihedral_angle_4_deg 18.663 r_dihedral_angle_3_deg 15.002 r_scangle_it 6.457 r_dihedral_angle_1_deg 5.396 r_scbond_it 5.082 r_mcangle_it 2.909 r_mcbond_it 1.969 r_angle_refined_deg 1.222 r_nbtor_refined 0.303 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.075 r_bond_refined_d 0.018 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2895 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 23
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