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Crystal structure of glucosamine-6-phosphate deaminase from Borrelia burgdorferi
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NE7 PDB entry 1NE7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.3 289 JCSG+ sparse matrix screen condition B12, 20% PEG 3350, 0.2 M Potassium phosphate pH 8.3, 27.2 mg/mL protein, 0.1 mg/mL Chymotrypsin, crystal tracking ID 203097b12, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.27 45.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.9 α = 90 b = 82.79 β = 109.58 c = 126.99 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 100 CCD RIGAKU SATURN 944+ 2009-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 2.2 50 96.1 0.054 20.75 85968 -3 31.993
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 2.2 2.26 85 0.245 5.6
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 1NE7 2.2 50 85951 4330 96.22 0.188 0.185 0.1867 0.237 0.1948 RANDOM 25.007
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] -0.16 -0.19 0.45 -0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.4 r_dihedral_angle_3_deg 15.448 r_dihedral_angle_4_deg 11.849 r_dihedral_angle_1_deg 5.845 r_scangle_it 3.679 r_scbond_it 2.24 r_mcangle_it 1.413 r_angle_refined_deg 1.378 r_mcbond_it 0.754 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.4 r_dihedral_angle_3_deg 15.448 r_dihedral_angle_4_deg 11.849 r_dihedral_angle_1_deg 5.845 r_scangle_it 3.679 r_scbond_it 2.24 r_mcangle_it 1.413 r_angle_refined_deg 1.378 r_mcbond_it 0.754 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12538 Nucleic Acid Atoms Solvent Atoms 855 Heterogen Atoms 27
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction