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N-Acetylmannosamine-6-phosphate 2-epimerase E180A from Staphylococcus aureus (strain MRSA USA300)
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 3.04 59.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.999 α = 90 b = 174.446 β = 90 c = 44.523 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 PIXEL DECTRIS EIGER X 16M 2018-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.95366 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 1.55 46.4 99.5 0.999 13.5 13.1 87948
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 1.55 1.57 0.842
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 1.55 42.004 87948 4414 99.449 0.152 0.1502 0.1643 0.1779 0.1895 19.856
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] -0.244 0.147 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.925 r_dihedral_angle_4_deg 29.585 r_dihedral_angle_3_deg 11.332 r_dihedral_angle_1_deg 6.282 r_lrange_it 6.166 r_lrange_other 6.166 r_scangle_it 4.307 r_scangle_other 4.306 r_scbond_it 2.813 r_scbond_other 2.812
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.925 r_dihedral_angle_4_deg 29.585 r_dihedral_angle_3_deg 11.332 r_dihedral_angle_1_deg 6.282 r_lrange_it 6.166 r_lrange_other 6.166 r_scangle_it 4.307 r_scangle_other 4.306 r_scbond_it 2.813 r_scbond_other 2.812 r_mcangle_other 2.398 r_mcangle_it 2.395 r_angle_refined_deg 1.905 r_mcbond_it 1.716 r_mcbond_other 1.693 r_angle_other_deg 1.56 r_nbd_refined 0.244 r_nbd_other 0.242 r_symmetry_nbd_refined 0.236 r_symmetry_xyhbond_nbd_refined 0.232 r_xyhbond_nbd_refined 0.21 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.168 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_symmetry_xyhbond_nbd_other 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3434 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing