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Crystal structure of phosphoserine phosphatase (SerB) from Brucella melitensis in complex with AP3 and magnesium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QPL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 PEG 3350, sodium malonate, Bis-Tris propane
Crystal Properties Matthews coefficient Solvent content 3.92 68.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 145.267 α = 90 b = 145.267 β = 90 c = 145.267 γ = 90
Symmetry Space Group I 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2023-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.980112 SOLEIL PROXIMA 2
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 2.74 45.94 99.86 0.1814 0.1837 0.02917 0.999 19.41 39.8 13539 64.9
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 2.74 2.84 99.03 1.504 1.523 0.2408 0.891 3.64 39.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.74 45.94 1.35 13526 677 99.89 0.1829 0.1802 0.2431 0.219 64.09
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.3918 f_angle_d 1.0842 f_chiral_restr 0.0573 f_bond_d 0.0089 f_plane_restr 0.0089
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2193 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 12
Software Software Software Name Purpose PHENIX refinement MxCuBE data collection XSCALE data scaling XDS data reduction Coot model building PHASER phasing