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Crystal structure of UrtA from Synechococcus CC9311 in complex with urea and calcium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.062 M MES; 0.038 imidazole, pH 6.5, 0.03M MgCl2, 0.03M CaCl2.2H2O, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD
Crystal Properties Matthews coefficient Solvent content 2.01 38.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.76 α = 90 b = 117.12 β = 90 c = 123.46 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 50 PIXEL DECTRIS PILATUS 12M 2020-06-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 3.0240, 3.3509, 4.2753, 4.7686 Diamond I23
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 1.97 85.114 93.3 0.076 0.08 0.026 0.999 22.8 15.6 49942
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 1.97 2.02 0.295 0.343 0.172 0.945 6.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 1.973 85.114 49942 2526 96.577 0.148 0.1467 0.1489 0.1737 0.1761 22.602
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] 0.669 0.378 -1.047
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.869 r_dihedral_angle_4_deg 18.648 r_dihedral_angle_3_deg 12.858 r_dihedral_angle_1_deg 6.739 r_lrange_it 5.03 r_lrange_other 5.025 r_scangle_it 4.077 r_scangle_other 4.077 r_scbond_it 2.796 r_scbond_other 2.795
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.869 r_dihedral_angle_4_deg 18.648 r_dihedral_angle_3_deg 12.858 r_dihedral_angle_1_deg 6.739 r_lrange_it 5.03 r_lrange_other 5.025 r_scangle_it 4.077 r_scangle_other 4.077 r_scbond_it 2.796 r_scbond_other 2.795 r_mcangle_it 2.365 r_mcangle_other 2.365 r_mcbond_it 1.862 r_mcbond_other 1.857 r_angle_refined_deg 1.64 r_angle_other_deg 1.415 r_nbd_other 0.274 r_nbd_refined 0.207 r_symmetry_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.182 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.172 r_metal_ion_refined 0.163 r_xyhbond_nbd_refined 0.153 r_symmetry_metal_ion_refined 0.134 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6217 Nucleic Acid Atoms Solvent Atoms 637 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement XDS data reduction Coot model building CRANK2 phasing XSCALE data scaling