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2.5A crystal structure of glucose/ribitol dehydrogenase from brucella melitensis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 289 20% PEG 3350, 0.15M DL MALIC ACID, pH 7.0, VAPOR DIFFUSION, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.25 45.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.489 α = 90 b = 147.939 β = 90 c = 63.892 γ = 90
Symmetry Space Group P 21 21 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 SATURN 944 MULTI-LAYER OPTICS MIRRORS 2008-01-01 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 2.5 50 94.8 0.133 8.978 3.4 31770
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) 2.5 2.59 95.8 0.571 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.5 50 30103 1598 94.72 0.20407 0.20063 0.2678 0.2468 RANDOM 39.237
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] -1.11 2.16 -1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.368 r_dihedral_angle_4_deg 20.238 r_dihedral_angle_3_deg 19.662 r_dihedral_angle_1_deg 6.309 r_scangle_it 2.613 r_scbond_it 1.584 r_angle_refined_deg 1.425 r_mcangle_it 1.053 r_mcbond_it 0.6 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.368 r_dihedral_angle_4_deg 20.238 r_dihedral_angle_3_deg 19.662 r_dihedral_angle_1_deg 6.309 r_scangle_it 2.613 r_scbond_it 1.584 r_angle_refined_deg 1.425 r_mcangle_it 1.053 r_mcbond_it 0.6 r_nbtor_refined 0.305 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.202 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.106 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7008 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction