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Crystal structure of a basic membrane lipoprotein from brucella melitensis, iodide soak
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other solved via SAD phasing based on iodide ions
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 25% PEG 3350, 100MM BISTRIS, 200MM NACL; BRABA.17960.A.A2, PS01053 AT 37.0MG/ML, CRYSTALS SOAKED FOR 30MIN IN 25% PEG 3350, 100M BISTRIS, 200MM NACL, 10% EG, 300MM NAI, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 5.50
Crystal Properties Matthews coefficient Solvent content 2.17 43.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.64 α = 90 b = 85.85 β = 90 c = 95.24 γ = 90
Symmetry Space Group C 2 2 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 RIGAKU SATURN 944+ 2011-05-23 M 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) 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 2.05 50 97.6 0.078 0.078 24.32 14 21344 -3 28.18
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 88.4 0.297 0.297 8.1 10.6 1581
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 solved via SAD phasing based on iodide ions 2.05 50 21867 20305 1093 97.9 0.179 0.179 0.177 0.1836 0.21 0.2111 RANDOM 17.67
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] -0.83 2.29 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_4_deg 16.183 r_dihedral_angle_3_deg 12.249 r_dihedral_angle_1_deg 5.666 r_scangle_it 2.985 r_scbond_it 1.972 r_angle_refined_deg 1.343 r_mcangle_it 1.168 r_angle_other_deg 0.888 r_mcbond_it 0.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_4_deg 16.183 r_dihedral_angle_3_deg 12.249 r_dihedral_angle_1_deg 5.666 r_scangle_it 2.985 r_scbond_it 1.972 r_angle_refined_deg 1.343 r_mcangle_it 1.168 r_angle_other_deg 0.888 r_mcbond_it 0.662 r_mcbond_other 0.177 r_chiral_restr 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2525 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 28
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling