☰ Navigation Tabs
Yeast Scavenger Decapping Enzyme in complex with m7GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XMM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 100 mM Hepes, 100 mM NaCl, 1.6 M AmSO4
Crystal Properties Matthews coefficient Solvent content 2.72 54.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.99 α = 90 b = 104.52 β = 90 c = 189.96 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 PIXEL DECTRIS PILATUS 6M 2009-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.0 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.25 20 99.1 0.079 0.089 12.57 2.31 83079 -3 50.217
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.31 99.5 0.716 0.851 2.32
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 1XMM 2.25 19.89 78749 4133 98.89 0.2228 0.2215 0.2129 0.2481 0.2425 RANDOM 54.795
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] -5.37 1.63 3.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_4_deg 21.417 r_dihedral_angle_3_deg 13.843 r_dihedral_angle_1_deg 5.934 r_mcangle_it 4.207 r_mcbond_it 3.134 r_mcbond_other 3.134 r_angle_refined_deg 1.354 r_angle_other_deg 1.214 r_chiral_restr 0.076
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.862 r_dihedral_angle_4_deg 21.417 r_dihedral_angle_3_deg 13.843 r_dihedral_angle_1_deg 5.934 r_mcangle_it 4.207 r_mcbond_it 3.134 r_mcbond_other 3.134 r_angle_refined_deg 1.354 r_angle_other_deg 1.214 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10329 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction