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Crystal structure of a ABC transporter, periplasmic substrate-binding protein from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PAM pdb entry 3pam modified with CCP4 program chainsaw
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 290 RigakuReagents JCSG+ screen, H3: 25% PEG 3350, 100mM BisTris, pH 5.5; cryo 20% EG; BrmeB.17356.a.B2.PS01888 at 17.1mg/ml, tray 248209h3, puck xtp3-5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.56 51.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.56 α = 90 b = 124.32 β = 90 c = 172.19 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 RAYONIX MX-300 2013-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.1 50 99.3 0.095 15.02 4.9 81772 81188 -3
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 2.1 2.15 99.8 0.434 3.15
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3pam modified with CCP4 program chainsaw 2.1 50 81772 77067 4054 99.3 0.15717 0.15509 0.1653 0.19603 0.2042 RANDOM 22.124
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] 0.78 -0.67 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.941 r_dihedral_angle_4_deg 19.379 r_dihedral_angle_3_deg 12.163 r_dihedral_angle_1_deg 6.396 r_scbond_it 1.576 r_mcangle_it 1.53 r_angle_refined_deg 1.514 r_angle_other_deg 1.061 r_mcbond_it 0.978 r_mcbond_other 0.974
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.941 r_dihedral_angle_4_deg 19.379 r_dihedral_angle_3_deg 12.163 r_dihedral_angle_1_deg 6.396 r_scbond_it 1.576 r_mcangle_it 1.53 r_angle_refined_deg 1.514 r_angle_other_deg 1.061 r_mcbond_it 0.978 r_mcbond_other 0.974 r_chiral_restr 0.089 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.005 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9237 Nucleic Acid Atoms Solvent Atoms 1211 Heterogen Atoms 30
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction