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EthR2 in complex with compound 9 (BDM76060)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.2M ammonium chloride, 0.1M MES, 20% (W/V) PEG600
Crystal Properties Matthews coefficient Solvent content 2.09 41.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.46 α = 90 b = 74.01 β = 90 c = 91.65 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 PILATUS3 2M 2017-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 1.0 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.69 57.58 99 0.056 14.25 4.6 45240
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.72 98.8 0.827 2.17 4.8
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 5N7O 1.69 57.58 42969 2271 98.96 0.21906 0.2175 0.2254 0.24885 0.2552 RANDOM 31.646
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] -0.02 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.216 r_dihedral_angle_4_deg 16.405 r_dihedral_angle_3_deg 12.055 r_long_range_B_refined 7.638 r_long_range_B_other 7.637 r_scangle_other 6.5 r_dihedral_angle_1_deg 4.862 r_scbond_it 4.252 r_scbond_other 4.251 r_mcangle_it 3.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.216 r_dihedral_angle_4_deg 16.405 r_dihedral_angle_3_deg 12.055 r_long_range_B_refined 7.638 r_long_range_B_other 7.637 r_scangle_other 6.5 r_dihedral_angle_1_deg 4.862 r_scbond_it 4.252 r_scbond_other 4.251 r_mcangle_it 3.252 r_mcangle_other 3.221 r_mcbond_it 2.48 r_mcbond_other 2.446 r_angle_refined_deg 1.593 r_angle_other_deg 1.534 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2915 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data scaling MOLREP phasing autoPROC data collection