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Structure of a periplasmic transporter
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.3 277 0.1M CdCl2, 0.1M sodium acetate, 30-32% (v/v) PEG 400 or 34-40% (v/v) PEG 200, pH 4.30, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.6 52.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.829 α = 90 b = 53.829 β = 90 c = 422.66 γ = 120
Symmetry Space Group P 65 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 MARMOSAIC 225 mm CCD 2005-10-20 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 2.3 15 96.6 0.079 6 9 15977
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) 2.3 2.36 72 0.125 5.3 8.7
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 (All) 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 2.3 15 15977 15977 863 96.61 0.18 0.18013 0.17633 0.1782 0.24924 0.2519 RANDOM 18.349
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] 0.05 0.02 0.05 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.437 r_dihedral_angle_4_deg 19.127 r_dihedral_angle_3_deg 15.607 r_sphericity_free 7.428 r_dihedral_angle_1_deg 6.445 r_scangle_it 4.06 r_scbond_it 2.716 r_sphericity_bonded 2.686 r_rigid_bond_restr 1.716 r_angle_refined_deg 1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.437 r_dihedral_angle_4_deg 19.127 r_dihedral_angle_3_deg 15.607 r_sphericity_free 7.428 r_dihedral_angle_1_deg 6.445 r_scangle_it 4.06 r_scbond_it 2.716 r_sphericity_bonded 2.686 r_rigid_bond_restr 1.716 r_angle_refined_deg 1.61 r_mcangle_it 1.598 r_mcbond_it 1.008 r_symmetry_hbond_refined 0.499 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.287 r_metal_ion_refined 0.229 r_xyhbond_nbd_refined 0.221 r_nbd_refined 0.209 r_chiral_restr 0.099 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2248 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction CCP4 data scaling SHELXS phasing