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Crystal structure of the N-acetyl-D-mannosamine dehydrogenase without substrates
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 2.21 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.255 α = 81.13 b = 59.062 β = 73.29 c = 74.206 γ = 79.25
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 MARMOSAIC 225 mm CCD 2011-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 1.9 12 90.5 0.06 6.2 1.9 63579 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 1.9 2 92.7 0.17 3.9 2
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 1.9 12 63579 3360 90.58 0.20966 0.20865 0.2261 0.22844 0.2441 RANDOM 27.924
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] -0.97 -0.43 -0.98 -0.65 -0.07 2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.958 r_dihedral_angle_3_deg 13.358 r_dihedral_angle_4_deg 11.769 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.226 r_scbond_it 1.982 r_angle_refined_deg 1.347 r_mcangle_it 1.147 r_angle_other_deg 1.053 r_mcbond_it 0.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.958 r_dihedral_angle_3_deg 13.358 r_dihedral_angle_4_deg 11.769 r_dihedral_angle_1_deg 6.018 r_scangle_it 3.226 r_scbond_it 1.982 r_angle_refined_deg 1.347 r_mcangle_it 1.147 r_angle_other_deg 1.053 r_mcbond_it 0.664 r_mcbond_other 0.184 r_chiral_restr 0.115 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.004 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_mcangle_other r_scbond_other 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 7170 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing