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Crystal structure of mRNA decapping enzyme (DcpS) from Mus musculus at 1.83 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ST0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 7.2 277 0.2M KF, 20.0% PEG-3350, No Buffer pH 7.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.35 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.399 α = 90 b = 59.231 β = 103.8 c = 100.14 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC 2003-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 ALS 5.0.3
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 1.83 37.58 97.9 0.063 18.07 3.69 64852 24.23
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) 1.83 1.9 84.84 0.389 3.04 3.07 5575
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1st0 1.83 37.58 61546 3300 97.69 0.16053 0.15838 0.1693 0.20101 0.2111 RANDOM 15.046
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] 0.07 0.28 0.31 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.324 r_dihedral_angle_4_deg 18.691 r_dihedral_angle_3_deg 13.137 r_dihedral_angle_1_deg 6.429 r_scangle_it 3.864 r_scbond_it 2.751 r_mcangle_it 1.798 r_angle_refined_deg 1.667 r_mcbond_it 1.289 r_angle_other_deg 1.036
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.324 r_dihedral_angle_4_deg 18.691 r_dihedral_angle_3_deg 13.137 r_dihedral_angle_1_deg 6.429 r_scangle_it 3.864 r_scbond_it 2.751 r_mcangle_it 1.798 r_angle_refined_deg 1.667 r_mcbond_it 1.289 r_angle_other_deg 1.036 r_mcbond_other 0.334 r_symmetry_vdw_other 0.282 r_symmetry_vdw_refined 0.225 r_nbd_refined 0.215 r_symmetry_hbond_refined 0.206 r_nbd_other 0.199 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.104 r_nbtor_other 0.087 r_bond_refined_d 0.018 r_xyhbond_nbd_other 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4885 Nucleic Acid Atoms Solvent Atoms 812 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement