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Crystal structure of a putative glucose 1-dehydrogenase from Burkholderia cenocepacia J2315
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JIG PDB ENTRY 4JIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 Morpheus G4:
37.5% MPD_P1K_P3350, 0.1M carboxylic acids, 0.1M buffer 1 pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.29 46.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.99 α = 90 b = 82.38 β = 90 c = 168.35 γ = 90
Symmetry Space Group P 21 21 21
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 RAYONIX MX300HE 2013-06-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 1.95 50 99.1 0.066 20.35 6.32 70830 70165 17.7
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 1.95 2 100 0.439 4.03 6.38 5164
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 4JIG 1.95 20 66568 3542 99.09 0.16069 0.15865 0.1689 0.19848 0.2028 RANDOM 26.232
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] -0.46 -0.54 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.574 r_dihedral_angle_4_deg 12.963 r_dihedral_angle_3_deg 11.285 r_dihedral_angle_1_deg 5.835 r_long_range_B_refined 5.47 r_long_range_B_other 5.347 r_scangle_other 3.214 r_mcangle_it 2.244 r_mcangle_other 2.243 r_scbond_it 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.574 r_dihedral_angle_4_deg 12.963 r_dihedral_angle_3_deg 11.285 r_dihedral_angle_1_deg 5.835 r_long_range_B_refined 5.47 r_long_range_B_other 5.347 r_scangle_other 3.214 r_mcangle_it 2.244 r_mcangle_other 2.243 r_scbond_it 2.07 r_scbond_other 2.07 r_angle_refined_deg 1.543 r_mcbond_it 1.525 r_mcbond_other 1.525 r_angle_other_deg 0.835 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6820 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 8
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling