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2.6 Angstrom Crystal Structure of the Complex Between the Nuclear SnoRNA Decapping Nudix Hydrolase X29 and Manganese in the Presence of 7-methyl-GDP
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 = 49.828 α = 90 b = 82.284 β = 90 c = 111.86 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 2004-08-23 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) R Sym 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 2.6 29.85 99.8 0.05 0.05 8.9 6.9 14734 14707 73.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.67 99.8 99.8 0.433 0.433 1.8 6.8 1071
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 2.6 27.6 14735 14223 1443 96.81 0.208 0.202 0.2123 0.258 RANDOM 60.844
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] 3.85 -0.74 -3.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_4_deg 17.905 r_dihedral_angle_3_deg 14.413 r_scangle_it 6.405 r_dihedral_angle_1_deg 5.08 r_scbond_it 4.449 r_mcangle_it 2.773 r_mcbond_it 1.715 r_angle_refined_deg 1.161 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.961 r_dihedral_angle_4_deg 17.905 r_dihedral_angle_3_deg 14.413 r_scangle_it 6.405 r_dihedral_angle_1_deg 5.08 r_scbond_it 4.449 r_mcangle_it 2.773 r_mcbond_it 1.715 r_angle_refined_deg 1.161 r_nbtor_refined 0.302 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.15 r_xyhbond_nbd_refined 0.12 r_chiral_restr 0.071 r_bond_refined_d 0.012 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2900 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement SCALA data scaling CNS refinement CCP4 data scaling CNS phasing MOSFLM data reduction