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Structure of ePepN E298A mutant in complex with Puromycin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 2.0M Sodium Malonate
Crystal Properties Matthews coefficient Solvent content 3.5 64.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.325 α = 90 b = 120.325 β = 90 c = 170.012 γ = 120
Symmetry Space Group P 31 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2015-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 19.9 99 2.13 4.3 49464
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 2HPO 2.5 19.9 46961 2503 99.41 0.12876 0.1258 0.1367 0.18427 0.19 RANDOM 33.438
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] 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.051 r_long_range_B_refined 34.869 r_long_range_B_other 34.867 r_dihedral_angle_4_deg 19.554 r_dihedral_angle_3_deg 15.064 r_dihedral_angle_1_deg 6.455 r_scangle_other 5.779 r_scbond_it 3.745 r_scbond_other 3.742 r_mcangle_it 3.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.051 r_long_range_B_refined 34.869 r_long_range_B_other 34.867 r_dihedral_angle_4_deg 19.554 r_dihedral_angle_3_deg 15.064 r_dihedral_angle_1_deg 6.455 r_scangle_other 5.779 r_scbond_it 3.745 r_scbond_other 3.742 r_mcangle_it 3.524 r_mcangle_other 3.523 r_mcbond_it 2.316 r_mcbond_other 2.316 r_angle_refined_deg 1.854 r_angle_other_deg 1.052 r_chiral_restr 0.106 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6936 Nucleic Acid Atoms Solvent Atoms 987 Heterogen Atoms 142
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing