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Crystal structure of protein BAD_0989 from Bifidobacterium adolescentis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 100mM HEPES pH 7.5, 10% PEG 3350, 200mM Proline, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.23 44.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.163 α = 90 b = 94.422 β = 90 c = 113.196 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 77 CCD MAR CCD 165 mm 2008-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 94.1 0.111 5.1 5.7 34422 -0.5 25.948
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 2.02 96.8 0.86 1.2 5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.1 20 24059 791 91.63 0.22417 0.22179 0.2215 0.29405 0.2909 RANDOM 25.915
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] -0.14 0.53 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.54 r_dihedral_angle_3_deg 18.441 r_dihedral_angle_4_deg 17.311 r_scangle_it 7.086 r_dihedral_angle_1_deg 5.118 r_scbond_it 4.92 r_mcangle_it 3.948 r_mcbond_it 2.661 r_angle_refined_deg 1.2 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.54 r_dihedral_angle_3_deg 18.441 r_dihedral_angle_4_deg 17.311 r_scangle_it 7.086 r_dihedral_angle_1_deg 5.118 r_scbond_it 4.92 r_mcangle_it 3.948 r_mcbond_it 2.661 r_angle_refined_deg 1.2 r_nbtor_refined 0.292 r_symmetry_hbond_refined 0.208 r_xyhbond_nbd_refined 0.18 r_nbd_refined 0.151 r_symmetry_vdw_refined 0.111 r_metal_ion_refined 0.092 r_chiral_restr 0.083 r_bond_refined_d 0.008 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_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 3362 Nucleic Acid Atoms Solvent Atoms 290 Heterogen Atoms 8
Software Software Software Name Purpose SHELXD phasing REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling