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Structure of periplasmic binding protein BugD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 278 Tris 10 mM, (NH4)2SO4 0.2 M, PEG1500 36% (w/v), glycerol 15%, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.43 49.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.67 α = 90 b = 76.42 β = 90 c = 260.86 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 MARMOSAIC 225 mm CCD 2004-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.72 49.63 99.8 0.072 7.1 10.9 101925 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.72 1.81 99.6 0.243 3 10.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) 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 1.72 49.63 102090 101925 5101 99.7 0.14 0.14 0.1445 0.175 0.1424 RANDOM 16.49
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] 0.45 -0.14 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.338 r_scangle_it 4.254 r_scbond_it 2.637 r_mcangle_it 1.379 r_angle_refined_deg 1.187 r_mcbond_it 0.761 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.127 r_xyhbond_nbd_refined 0.114
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.338 r_scangle_it 4.254 r_scbond_it 2.637 r_mcangle_it 1.379 r_angle_refined_deg 1.187 r_mcbond_it 0.761 r_nbd_refined 0.201 r_symmetry_vdw_refined 0.186 r_symmetry_hbond_refined 0.127 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined 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 6750 Nucleic Acid Atoms Solvent Atoms 1107 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction CCP4 data scaling SHARP phasing