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Structure of the E. coli MacB periplasmic domain (P21)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 30% Pentaerythritol ethoxylate (15/4 EO/OH), 6% polyvinylpyrrolidone, 100mM HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.94 36.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.11 α = 90 b = 54.86 β = 92.86 c = 66.89 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2014-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.96861 Diamond I24
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 1.95 66.81 99.8 0.089 8.1 3.4 25260
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3ftj 1.95 32.87 25260 1309 99.76 0.18043 0.17796 0.1899 0.22772 0.2381 RANDOM 25.77
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] 2.24 -0.89 -1.3
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.744 r_long_range_B_other 6.662 r_scangle_other 4.931 r_mcangle_other 3.427 r_mcangle_it 3.426 r_scbond_it 3.188 r_scbond_other 3.188 r_mcbond_it 2.287 r_mcbond_other 2.287 r_angle_refined_deg 1.659
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 6.744 r_long_range_B_other 6.662 r_scangle_other 4.931 r_mcangle_other 3.427 r_mcangle_it 3.426 r_scbond_it 3.188 r_scbond_other 3.188 r_mcbond_it 2.287 r_mcbond_other 2.287 r_angle_refined_deg 1.659 r_angle_other_deg 1.234 r_chiral_restr 0.095 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.005 r_dihedral_angle_1_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3181 Nucleic Acid Atoms Solvent Atoms 99 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing