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2.45 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29, Manganese and 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 = 49.998 α = 90 b = 82.553 β = 90 c = 112.16 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 2005-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 38.74 91.9 0.057 25.4 11.34 17738 16302 54.6
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 2.45 2.54 91.3 91.3 0.343 6.9 10.04 1737
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 38.74 17692 16269 1620 91.94 0.217 0.211 0.2223 0.265 RANDOM 52.338
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] 4.5 -1.48 -3.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.92 r_dihedral_angle_4_deg 17.413 r_dihedral_angle_3_deg 15.202 r_dihedral_angle_1_deg 5.146 r_scangle_it 5.035 r_scbond_it 3.392 r_mcangle_it 2.05 r_mcbond_it 1.249 r_angle_refined_deg 1.139 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.92 r_dihedral_angle_4_deg 17.413 r_dihedral_angle_3_deg 15.202 r_dihedral_angle_1_deg 5.146 r_scangle_it 5.035 r_scbond_it 3.392 r_mcangle_it 2.05 r_mcbond_it 1.249 r_angle_refined_deg 1.139 r_nbtor_refined 0.297 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.17 r_xyhbond_nbd_refined 0.123 r_symmetry_hbond_refined 0.086 r_chiral_restr 0.068 r_bond_refined_d 0.018 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2940 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 72
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