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Crystal structure of the N-acetyl-D-mannosamine dehydrogenase with n-acetylmannosamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D1Y PDB ENTRY 2D1Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 0.1 M HEPES, PH 7.5 AND 30% (W/V) PEG [POLY(ETHYLENE GLYCOL)] 300
Crystal Properties Matthews coefficient Solvent content 2.2 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.39 α = 67.43 b = 100.12 β = 89.75 c = 111.6 γ = 72.46
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 294 CCD ADSC QUANTUM 210r 2011-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 15 96.9 0.09 5.2 2.5 189715 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.27 97.8 0.36 1.7 2.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2D1Y 2.15 15 189715 10032 97.73 0.20225 0.20074 0.2026 0.23102 0.2317 RANDOM 22.534
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] -0.38 2 0.21 -1.81 1.34 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.804 r_dihedral_angle_4_deg 14.487 r_dihedral_angle_3_deg 14.254 r_dihedral_angle_1_deg 6.184 r_angle_refined_deg 1.333 r_angle_other_deg 1.068 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.804 r_dihedral_angle_4_deg 14.487 r_dihedral_angle_3_deg 14.254 r_dihedral_angle_1_deg 6.184 r_angle_refined_deg 1.333 r_angle_other_deg 1.068 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29105 Nucleic Acid Atoms Solvent Atoms 811 Heterogen Atoms 392
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing