☰ Navigation Tabs
N-Acetylmannosamine-6-phosphate 2-epimerase from Staphylococcus aureus (strain MRSA USA300) with 5-deoxy substrate 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 2.97 58.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.437 α = 90 b = 173.454 β = 90 c = 44.04 γ = 90
Symmetry Space Group P 21 21 2
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 210r 2017-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX1 0.95370 Australian Synchrotron MX1
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 1.88 46.11 99.67 0.998 10.1 7.2 48503
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 1.88 1.95 0.702
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6VVA 1.88 46.11 48503 2470 99.659 0.156 0.1539 0.1967 0.1797 21.308
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] 0.164 -0.539 0.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.375 r_dihedral_angle_4_deg 27.51 r_dihedral_angle_3_deg 11.76 r_dihedral_angle_1_deg 6.501 r_lrange_it 6.109 r_lrange_other 5.901 r_scangle_it 4.207 r_scangle_other 4.206 r_scbond_it 2.708 r_scbond_other 2.708
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.375 r_dihedral_angle_4_deg 27.51 r_dihedral_angle_3_deg 11.76 r_dihedral_angle_1_deg 6.501 r_lrange_it 6.109 r_lrange_other 5.901 r_scangle_it 4.207 r_scangle_other 4.206 r_scbond_it 2.708 r_scbond_other 2.708 r_mcangle_other 2.363 r_mcangle_it 2.356 r_mcbond_it 1.647 r_mcbond_other 1.639 r_angle_refined_deg 1.632 r_angle_other_deg 1.455 r_symmetry_xyhbond_nbd_refined 0.226 r_nbd_refined 0.216 r_symmetry_nbd_refined 0.213 r_xyhbond_nbd_refined 0.208 r_nbd_other 0.189 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.169 r_chiral_restr 0.084 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.07 r_bond_refined_d 0.012 r_xyhbond_nbd_other 0.009 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3442 Nucleic Acid Atoms Solvent Atoms 581 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing