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The structure of EntE with 2-nitrobenzoyl adenylate analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 2-methyl-2,4-pentanediol, HEPES-Na, 2-nitrobenzoyl-AMS
Crystal Properties Matthews coefficient Solvent content 2.6 52.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.503 α = 90 b = 57.22 β = 96.31 c = 171.648 γ = 90
Symmetry Space Group I 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 2018-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 50 99.7 0.064 0.088 0.06 0.997 9.1 3.3 44501 30.106
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.54 99.9 0.386 0.525 0.355 0.863 2.1 3.4
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 3RG2 2.45 45.34 42264 2235 99.63 0.19123 0.18864 0.1951 0.24075 0.2451 RANDOM 33.975
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] 1.81 2.54 -2.54 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.237 r_dihedral_angle_4_deg 17.069 r_dihedral_angle_3_deg 14.691 r_dihedral_angle_1_deg 6.034 r_angle_refined_deg 1.502 r_angle_other_deg 0.935 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.237 r_dihedral_angle_4_deg 17.069 r_dihedral_angle_3_deg 14.691 r_dihedral_angle_1_deg 6.034 r_angle_refined_deg 1.502 r_angle_other_deg 0.935 r_chiral_restr 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.004 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8124 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing