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Crystal structure of YrbI lacking the last 8 residues, in complex with Kdo and inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R8E PDB CODE: 2R8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 294 1.875 M Ammonium Sulfate, 100mM Na Cacodylate pH 6.5,
2.5% glycerol, stoichiometric amount of Kdo8P (cleaved upon incubation in the drop), VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.22 44.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.964 α = 90 b = 144.104 β = 90 c = 145.854 γ = 90
Symmetry Space Group C 2 2 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 300 mm CCD 2007-12-06
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.49 50 92.7 0.125 8.9 4.1 21494 2.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.49 2.65 94.2 0.46 2.3 3.9
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 PDB CODE: 2R8E 2.49 40 21494 1132 92.7 0.202 0.2 0.1992 0.238 0.2378 RANDOM 24.34
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 -0.17 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.421 r_dihedral_angle_4_deg 17.965 r_dihedral_angle_3_deg 14.727 r_dihedral_angle_1_deg 4.855 r_scangle_it 1.799 r_scbond_it 1.137 r_angle_refined_deg 1.072 r_mcangle_it 0.633 r_mcbond_it 0.491 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.421 r_dihedral_angle_4_deg 17.965 r_dihedral_angle_3_deg 14.727 r_dihedral_angle_1_deg 4.855 r_scangle_it 1.799 r_scbond_it 1.137 r_angle_refined_deg 1.072 r_mcangle_it 0.633 r_mcbond_it 0.491 r_nbtor_refined 0.298 r_nbd_refined 0.203 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_refined 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5198 Nucleic Acid Atoms Solvent Atoms 188 Heterogen Atoms 56
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling