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Synthetic Gene Encoded DcpS bound to inhibitor DG153249
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ST0 PDB ENTRY 1ST0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 PEG 3350, Ammonium Formate, vapor diffusion, hanging drop, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.1 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.73 α = 117.68 b = 55.812 β = 93.35 c = 59.4 γ = 99.72
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 RIGAKU SATURN 944 mirrors 2007-09-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54178
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 2.6 50 96.3 0.104 9.7 2 15959 1 1
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) 2.6 2.69 94.3 0.467 2 2 1567
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 PDB ENTRY 1ST0 2.6 32.84 15958 799 95.8 0.213 0.21 0.2157 0.278 0.2277 RANDOM 27.094
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] 0.39 0.33 1.92 -0.34 -0.26 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.881 r_dihedral_angle_4_deg 20.378 r_dihedral_angle_3_deg 16.919 r_dihedral_angle_1_deg 6.113 r_angle_refined_deg 1.121 r_scangle_it 1.082 r_angle_other_deg 0.828 r_scbond_it 0.684 r_mcangle_it 0.529 r_mcbond_it 0.473
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.881 r_dihedral_angle_4_deg 20.378 r_dihedral_angle_3_deg 16.919 r_dihedral_angle_1_deg 6.113 r_angle_refined_deg 1.121 r_scangle_it 1.082 r_angle_other_deg 0.828 r_scbond_it 0.684 r_mcangle_it 0.529 r_mcbond_it 0.473 r_nbd_refined 0.209 r_nbd_other 0.188 r_symmetry_vdw_other 0.178 r_nbtor_refined 0.176 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.147 r_symmetry_hbond_refined 0.096 r_nbtor_other 0.082 r_chiral_restr 0.062 r_mcbond_other 0.049 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4755 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 44
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HTCollect data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing