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EthR2 in complex with compound 1 (BDM14272)
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 4.2 293 0.2 M NaCl, 0.2 M Na citrate and 15% (W/V) PEG-MME 5000
Crystal Properties Matthews coefficient Solvent content 2.05 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.81 α = 90 b = 74.57 β = 90 c = 88.78 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 CCD RIGAKU SATURN 944 2014-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.541870
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 2.45 30 99.4 0.235 9.65 6.99 15012
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 2.45 2.6 97.5 1.203 2.04 6.57
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5N7O 2.45 27.76 14261 751 99.38 0.21883 0.21573 0.27949 0.233 RANDOM 32.698
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] 0.04 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.138 r_dihedral_angle_4_deg 19.658 r_dihedral_angle_3_deg 15.555 r_long_range_B_refined 7.19 r_long_range_B_other 7.189 r_dihedral_angle_1_deg 5.562 r_scangle_other 5.539 r_mcangle_other 4.065 r_mcangle_it 4.064 r_scbond_it 3.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.138 r_dihedral_angle_4_deg 19.658 r_dihedral_angle_3_deg 15.555 r_long_range_B_refined 7.19 r_long_range_B_other 7.189 r_dihedral_angle_1_deg 5.562 r_scangle_other 5.539 r_mcangle_other 4.065 r_mcangle_it 4.064 r_scbond_it 3.585 r_scbond_other 3.585 r_mcbond_other 2.738 r_mcbond_it 2.737 r_angle_refined_deg 1.74 r_angle_other_deg 1.326 r_chiral_restr 0.077 r_bond_refined_d 0.01 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 2914 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building MOLREP phasing