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Structure and kinetics of a monomeric glucosamine-6-phosphate deaminase: missing link of the NagB superfamily
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DEA PDB EBTRY 1DEA
Crystallization Crystal Properties Matthews coefficient Solvent content 1.9 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.009 α = 90 b = 48.023 β = 91.04 c = 71.761 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.5 30 98.8 0.14 14.6 5.6 67231 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 1.5 1.55 97.7 0.43 4.6 3.6
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 EBTRY 1DEA 1.5 72.55 67204 3401 98.3 0.167 0.165 0.1734 0.211 0.1908 RANDOM 10.78
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] -0.632 -0.434 -0.119 0.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.859 r_dihedral_angle_4_deg 16.111 r_dihedral_angle_3_deg 14.667 r_dihedral_angle_1_deg 5.684 r_scangle_it 5.491 r_scbond_it 4.193 r_mcangle_it 2.418 r_mcbond_it 2.058 r_angle_refined_deg 1.698 r_symmetry_vdw_refined 0.263
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.859 r_dihedral_angle_4_deg 16.111 r_dihedral_angle_3_deg 14.667 r_dihedral_angle_1_deg 5.684 r_scangle_it 5.491 r_scbond_it 4.193 r_mcangle_it 2.418 r_mcbond_it 2.058 r_angle_refined_deg 1.698 r_symmetry_vdw_refined 0.263 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.19 r_nbtor_refined 0.178 r_symmetry_hbond_refined 0.175 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_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 3789 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing