☰ Navigation Tabs
Crystal structure of D38C glucose dehydrogenase mutant from Haloferax mediterranei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B5V PDB ENTRY 2B5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 290 pH 7.00, temperature 290K, Vapor diffusion, hanging drop, VAPOR DIFFUSION, HANGING DROP, temperature 290 KK
Crystal Properties Matthews coefficient Solvent content 3.2 61.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.534 α = 90 b = 109.255 β = 90 c = 151.893 γ = 90
Symmetry Space Group I 2 2 2
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 ADSC QUANTUM 4 MIRRORS 2002-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 1.6 20 99.1 0.058 25.85 5.1 66155
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 1.6 1.64 98.2 0.543 2.69
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-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 2B5V 1.6 20 62795 3356 98.8 0.154 0.1728 0.186 0.1999 RANDOM 21.16
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 16.687 r_scbond_it 14.42 r_mcangle_it 7.136 r_mcbond_it 5.986 r_dihedral_angle_1_deg 5.621 r_angle_refined_deg 1.555 r_angle_other_deg 0.854 r_symmetry_vdw_other 0.298 r_symmetry_hbond_refined 0.286 r_symmetry_vdw_refined 0.276
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 16.687 r_scbond_it 14.42 r_mcangle_it 7.136 r_mcbond_it 5.986 r_dihedral_angle_1_deg 5.621 r_angle_refined_deg 1.555 r_angle_other_deg 0.854 r_symmetry_vdw_other 0.298 r_symmetry_hbond_refined 0.286 r_symmetry_vdw_refined 0.276 r_nbd_other 0.245 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.19 r_chiral_restr 0.094 r_metal_ion_refined 0.092 r_nbtor_other 0.086 r_bond_refined_d 0.023 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2767 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 67
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement