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Crystal structure of YrbI from Escherichia coli in complex with Mg
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.7 54.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.877 α = 118.84 b = 83.005 β = 118.77 c = 85.864 γ = 90.06
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 225 mm CCD 2007-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.97869 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 40 313166
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.4 29.34 296631 15726 94.72 0.1601 0.1586 0.1573 0.18807 0.1868 RANDOM 21.281
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] -0.05 -0.08 -0.2 0.11 -0.02 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.304 r_dihedral_angle_4_deg 17.278 r_dihedral_angle_3_deg 12.925 r_dihedral_angle_1_deg 6.257 r_sphericity_free 4.393 r_sphericity_bonded 4.045 r_scangle_it 3.622 r_scbond_it 2.688 r_rigid_bond_restr 1.845 r_mcangle_it 1.673
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.304 r_dihedral_angle_4_deg 17.278 r_dihedral_angle_3_deg 12.925 r_dihedral_angle_1_deg 6.257 r_sphericity_free 4.393 r_sphericity_bonded 4.045 r_scangle_it 3.622 r_scbond_it 2.688 r_rigid_bond_restr 1.845 r_mcangle_it 1.673 r_angle_refined_deg 1.368 r_mcbond_it 1.11 r_nbtor_refined 0.313 r_symmetry_vdw_refined 0.28 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.207 r_chiral_restr 0.134 r_symmetry_hbond_refined 0.11 r_bond_refined_d 0.01 r_metal_ion_refined 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10564 Nucleic Acid Atoms Solvent Atoms 2232 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement