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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 2BKV PDB ENTRY 2BKV
Crystallization Crystal Properties Matthews coefficient Solvent content 1.66 25.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.966 α = 90 b = 47.898 β = 90.06 c = 71.397 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 ID14-1 ESRF ID14-1
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 1.4 30 92.9 0.06 15.83 3.6 78148 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 1.4 1.45 61.6 0.31 4.31 3.2
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 2BKV 1.4 70.71 78127 3898 92.7 0.122 0.119 0.1299 0.165 0.1506 RANDOM 9.8
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] 0.059 -0.071 -0.162 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.514 r_dihedral_angle_4_deg 14.947 r_dihedral_angle_3_deg 13.532 r_dihedral_angle_1_deg 5.76 r_scangle_it 5.122 r_scbond_it 3.866 r_mcangle_it 2.194 r_mcbond_it 1.985 r_angle_other_deg 1.972 r_angle_refined_deg 1.658
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.514 r_dihedral_angle_4_deg 14.947 r_dihedral_angle_3_deg 13.532 r_dihedral_angle_1_deg 5.76 r_scangle_it 5.122 r_scbond_it 3.866 r_mcangle_it 2.194 r_mcbond_it 1.985 r_angle_other_deg 1.972 r_angle_refined_deg 1.658 r_nbd_refined 0.238 r_symmetry_vdw_refined 0.223 r_symmetry_vdw_other 0.206 r_nbd_other 0.203 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.176 r_chiral_restr 0.116 r_nbtor_other 0.098 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 3796 Nucleic Acid Atoms Solvent Atoms 730 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing