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EthR2 in complex with compound 5 (BDM71847)
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 293 0.2-0.4M ammonium chloride, 0.1M MES, 20% (W/V) PEG600
Crystal Properties Matthews coefficient Solvent content 2.5 50.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.09 α = 90 b = 40.56 β = 96.75 c = 108.74 γ = 90
Symmetry Space Group C 1 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 PIXEL DECTRIS PILATUS3 2M 2017-10-27 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 1.45 107.99 95.4 0.045 13.95 2.7 80773
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 1.45 1.48 98.3 0.57 2.23 2.4
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 1.45 107.99 76725 4048 95.4 0.19848 0.19749 0.1975 0.21732 0.217 RANDOM 19.909
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 25.162 r_dihedral_angle_4_deg 15.665 r_dihedral_angle_3_deg 11.251 r_long_range_B_refined 5.298 r_long_range_B_other 5.292 r_dihedral_angle_1_deg 4.706 r_scangle_other 4.701 r_scbond_it 3.172 r_scbond_other 3.171 r_mcangle_it 2.193
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.162 r_dihedral_angle_4_deg 15.665 r_dihedral_angle_3_deg 11.251 r_long_range_B_refined 5.298 r_long_range_B_other 5.292 r_dihedral_angle_1_deg 4.706 r_scangle_other 4.701 r_scbond_it 3.172 r_scbond_other 3.171 r_mcangle_it 2.193 r_mcangle_other 2.193 r_angle_refined_deg 1.799 r_mcbond_it 1.636 r_mcbond_other 1.636 r_angle_other_deg 1.591 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 3017 Nucleic Acid Atoms Solvent Atoms 240 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data scaling MOLREP phasing autoPROC data collection