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Crystal Structure of Xenopus laevis nudix hydrolase nuclear SnoRNA decapping Protein X29
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.68 295 0.025 M HEPES, 3.75% PEG 6000, pH 7.68, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.27 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.188 α = 90 b = 82.99 β = 90 c = 111.063 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 II Osmic Confocal optics 2004-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 26.8 0.054 7.1 6.8 27307 27224 46.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.15 99.1 0.355 2.1 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT 2.1 26.9 27273 24464 2701 99.68 0.20881 0.20404 0.2113 0.25421 RANDOM 38.719
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] 2.4 -1.18 -1.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 3.771 r_scangle_it 3.498 r_scbond_it 2.084 r_mcangle_it 1.603 r_angle_refined_deg 1.108 r_mcbond_it 0.86 r_symmetry_vdw_refined 0.216 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.079
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 3.771 r_scangle_it 3.498 r_scbond_it 2.084 r_mcangle_it 1.603 r_angle_refined_deg 1.108 r_mcbond_it 0.86 r_symmetry_vdw_refined 0.216 r_nbd_refined 0.212 r_xyhbond_nbd_refined 0.117 r_chiral_restr 0.079 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 3037 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SOLVE phasing SHARP phasing