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Crystal structure of UrtA1 from Synechococcus WH8102 in complex with urea and calcium
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.05 M Sodium Hepes: MOPS pH 7.5, 0.03 MgCl2, 0.03 CaCl2; 20 % PEG 500 MME; 10 % Peg 20000 Cryo: 30 % Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.29 46.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.51 α = 90 b = 71.39 β = 90 c = 120.46 γ = 90
Symmetry Space Group P 21 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 50 PIXEL DECTRIS PILATUS 12M 2020-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 2.7552 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 1.8 120.46 91.3 0.156 0.16 0.032 0.999 18 38.4 35399
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 1.8 1.84 76 2.902 3.139 1.122 0.161 12.5
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 1.8 71.492 35358 1775 91.131 0.161 0.159 0.1557 0.1903 0.1812 33.343
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] 0.777 0.797 -1.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.76 r_dihedral_angle_3_deg 14.113 r_dihedral_angle_4_deg 10.763 r_dihedral_angle_1_deg 6.913 r_lrange_it 5.897 r_lrange_other 5.862 r_scangle_it 5.09 r_scangle_other 5.089 r_scbond_it 3.531 r_scbond_other 3.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.76 r_dihedral_angle_3_deg 14.113 r_dihedral_angle_4_deg 10.763 r_dihedral_angle_1_deg 6.913 r_lrange_it 5.897 r_lrange_other 5.862 r_scangle_it 5.09 r_scangle_other 5.089 r_scbond_it 3.531 r_scbond_other 3.53 r_mcangle_it 2.854 r_mcangle_other 2.854 r_mcbond_it 2.299 r_mcbond_other 2.298 r_angle_refined_deg 1.612 r_angle_other_deg 1.409 r_symmetry_xyhbond_nbd_refined 0.228 r_nbd_refined 0.2 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.171 r_nbd_other 0.158 r_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.127 r_metal_ion_refined 0.106 r_chiral_restr 0.085 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.015 r_symmetry_metal_ion_refined 0.012 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3064 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling CRANK2 phasing Coot model building