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Crystal Structure of a Ribulose-phosphate 3-epimerase from Neisseria gonorrhoeae with bound phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3INP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 290 NegoA.18161.a.B1.PS38017 at 26.22 mg/ml mixed 1:1 with an equal volume Morpheus (b3): 10% (w/v) PEG-4000, 20% (v/v) glycerol, 0.1 M MES/imidazole, pH=6.5, 0.03 M each sodium fluoride, sodium bromide, sodium iodide
Crystal Properties Matthews coefficient Solvent content 2.25 45.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.73 α = 90 b = 70.9 β = 109.31 c = 83.5 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 100 CCD MARMOSAIC 300 mm CCD Beryllium Lenses 2016-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.4 40.684 99.8 0.07 0.082 0.996 11.09 3.749 132656 -3 12.94
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.44 99.9 0.538 0.631 0.798 2.34 3.698 16492
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3INP 1.4 40.684 1.35 132647 2019 99.87 0.1487 0.1484 0.1496 0.1648 0.1665 18.9641
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 18.589 f_angle_d 0.844 f_chiral_restr 0.087 f_plane_restr 0.006 f_bond_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5028 Nucleic Acid Atoms Solvent Atoms 806 Heterogen Atoms 48
Software Software Software Name Purpose XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction XDS data reduction MoRDa phasing