☰ Navigation Tabs
1.9 Angstrom Resolution Crystal Structure of Maltose-Binding Periplasmic Protein MalE from Listeria monocytogenes in Complex with Maltose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XD3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Protein: 15.2 mg/ml, 0.5M Sodium chloride, 0.01M Tris HCl (pH 8.3), 2mM MAL;
Screen: Classics II (C2), 1.1M Ammonium tartrate (pH 7.0).
Crystal Properties Matthews coefficient Solvent content 2.36 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.208 α = 90 b = 78.452 β = 90 c = 90.69 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 300 mm CCD C(111) 2016-10-27 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) 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 1.9 30 100 0.081 0.081 34.4 7 33694 -3 29.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.779 0.826 2.9 6.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2XD3 1.9 29.67 31867 1557 99.94 0.17603 0.17436 0.20823 0.2103 RANDOM 33.167
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] -2.25 0.21 2.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.263 r_dihedral_angle_4_deg 10.16 r_dihedral_angle_3_deg 9.657 r_long_range_B_refined 5.345 r_long_range_B_other 5.227 r_dihedral_angle_1_deg 3.12 r_scangle_other 2.411 r_scbond_it 1.508 r_scbond_other 1.504 r_mcangle_it 1.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.263 r_dihedral_angle_4_deg 10.16 r_dihedral_angle_3_deg 9.657 r_long_range_B_refined 5.345 r_long_range_B_other 5.227 r_dihedral_angle_1_deg 3.12 r_scangle_other 2.411 r_scbond_it 1.508 r_scbond_other 1.504 r_mcangle_it 1.494 r_mcangle_other 1.493 r_angle_refined_deg 1.339 r_mcbond_it 0.943 r_mcbond_other 0.943 r_angle_other_deg 0.866 r_chiral_restr 0.089 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.009 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3007 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing