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N-Acetylmannosamine-6-phosphate 2-epimerase from Staphylococcus aureus (strain MRSA USA300) with substrate and product bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6VVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 1 M trisodium citrate, 0.1 M sodium cacodylate, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.98 58.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.928 α = 90 b = 76.474 β = 90 c = 174.207 γ = 90
Symmetry Space Group P 2 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 100 CCD ADSC QUANTUM 315r 2016-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95369 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.51 46.25 98.73 0.998 17.5 30.1 91961
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.56 0.661
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT FREE R-VALUE 6VVA 1.51 46.25 91961 4620 98.725 0.181 0.1798 0.1902 0.2099 0.2213 12.515
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] 0.624 -0.207 -0.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.112 r_dihedral_angle_4_deg 31.125 r_dihedral_angle_3_deg 12.448 r_dihedral_angle_1_deg 6.5 r_lrange_it 6.185 r_lrange_other 6.131 r_scangle_it 2.877 r_scangle_other 2.876 r_mcangle_other 1.916 r_mcangle_it 1.915
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.112 r_dihedral_angle_4_deg 31.125 r_dihedral_angle_3_deg 12.448 r_dihedral_angle_1_deg 6.5 r_lrange_it 6.185 r_lrange_other 6.131 r_scangle_it 2.877 r_scangle_other 2.876 r_mcangle_other 1.916 r_mcangle_it 1.915 r_scbond_it 1.85 r_scbond_other 1.849 r_angle_refined_deg 1.844 r_angle_other_deg 1.477 r_mcbond_it 1.206 r_mcbond_other 1.199 r_symmetry_xyhbond_nbd_refined 0.253 r_nbd_refined 0.24 r_xyhbond_nbd_refined 0.237 r_nbd_other 0.212 r_symmetry_nbd_other 0.195 r_symmetry_nbd_refined 0.185 r_nbtor_refined 0.166 r_chiral_restr 0.094 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3440 Nucleic Acid Atoms Solvent Atoms 596 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing