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Crystal structure of PhnD from Synechococcus MITS9220 in complex with phosphate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 0.1M Tris pH 8.5, 25 % PEG 3350, 30 % Ethylene Glycol
Crystal Properties Matthews coefficient Solvent content 2.28 46.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.59 α = 90 b = 40.67 β = 92.13 c = 106.68 γ = 90
Symmetry Space Group C 1 2 1
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 2020-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I23 3.09960, 2.7552, 4.8621, 5.1660 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 1.8 106.606 69.8 0.062 0.068 0.027 0.999 17.1 10.3 18073
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 0.58 0.714 0.408 0.939 5.1
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 2.02 106.606 18073 931 99.291 0.154 0.1528 0.1525 0.1763 0.1752 19.19
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] 1.602 -0.925 0.004 -1.533
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.088 r_dihedral_angle_4_deg 20.689 r_dihedral_angle_3_deg 13.38 r_dihedral_angle_1_deg 7.024 r_lrange_it 6.396 r_lrange_other 6.273 r_scangle_it 4.649 r_scangle_other 4.648 r_scbond_it 2.999 r_scbond_other 2.998
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.088 r_dihedral_angle_4_deg 20.689 r_dihedral_angle_3_deg 13.38 r_dihedral_angle_1_deg 7.024 r_lrange_it 6.396 r_lrange_other 6.273 r_scangle_it 4.649 r_scangle_other 4.648 r_scbond_it 2.999 r_scbond_other 2.998 r_mcangle_other 2.554 r_mcangle_it 2.553 r_mcbond_it 1.801 r_mcbond_other 1.799 r_angle_refined_deg 1.725 r_angle_other_deg 1.448 r_symmetry_xyhbond_nbd_refined 0.236 r_nbd_refined 0.212 r_nbd_other 0.184 r_symmetry_nbd_other 0.182 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.081 r_symmetry_nbd_refined 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2129 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling CRANK2 phasing Coot model building