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Crystal structure of Eed in complex with NDSB-195
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other SeMet EED structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 291 4M Sodium formate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.67 53.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.803 α = 90 b = 85.337 β = 90 c = 91.231 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 MARMOSAIC 225 mm CCD Vertically collimating premirror, double crystal Si(111) monochromator with sagital focussing, vertical focusing mirror M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.9790 SRS PX10.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (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 1.95 30 98.5 0.091 0.091 14.5 4.4 31920 31920 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.95 2.02 91 0.426 0.426 2.1 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SeMet EED structure 1.95 27.56 31442 31442 1680 98.55 0.19724 0.19724 0.19539 0.1977 0.23156 0.2325 RANDOM 21.715
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 -0.02 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.242 r_dihedral_angle_4_deg 19.369 r_dihedral_angle_3_deg 14.369 r_dihedral_angle_1_deg 7.254 r_scangle_it 4.087 r_scbond_it 2.737 r_mcangle_it 1.782 r_angle_refined_deg 1.68 r_mcbond_it 1.15 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.242 r_dihedral_angle_4_deg 19.369 r_dihedral_angle_3_deg 14.369 r_dihedral_angle_1_deg 7.254 r_scangle_it 4.087 r_scbond_it 2.737 r_mcangle_it 1.782 r_angle_refined_deg 1.68 r_mcbond_it 1.15 r_nbtor_refined 0.301 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.124 r_chiral_restr 0.119 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2895 Nucleic Acid Atoms Solvent Atoms 238 Heterogen Atoms 12
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling