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Structural Insights into the Mechanism of Escherichia coli Ymdb
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SPV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 285 2 M ammonium sulfate, 0.1 M BIS-TRIS
Crystal Properties Matthews coefficient Solvent content 3.89 68.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 289.14 α = 90 b = 289.14 β = 90 c = 114.053 γ = 120
Symmetry Space Group P 31 2 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 CCD ADSC QUANTUM 315r 2015-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9791 SSRF BL17U
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 2.8 50 98.9 0.114 12.7 3.6 133057
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 2.8 2.85 98.9 0.386 3.1 3.3
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 1SPV 2.8 38.72 126269 6667 98.85 0.26296 0.26153 0.2624 0.29036 0.2913 RANDOM 38.947
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] 0.04 0.04 0.04 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.852 r_dihedral_angle_4_deg 21.846 r_dihedral_angle_3_deg 21.363 r_long_range_B_refined 6.804 r_long_range_B_other 6.804 r_dihedral_angle_1_deg 5.385 r_mcangle_it 4.274 r_mcangle_other 4.274 r_scangle_other 4.047 r_angle_other_deg 3.865
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.852 r_dihedral_angle_4_deg 21.846 r_dihedral_angle_3_deg 21.363 r_long_range_B_refined 6.804 r_long_range_B_other 6.804 r_dihedral_angle_1_deg 5.385 r_mcangle_it 4.274 r_mcangle_other 4.274 r_scangle_other 4.047 r_angle_other_deg 3.865 r_mcbond_it 2.672 r_mcbond_other 2.671 r_scbond_it 2.535 r_scbond_other 2.535 r_angle_refined_deg 1.896 r_chiral_restr 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 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 22926 Nucleic Acid Atoms Solvent Atoms 214 Heterogen Atoms 756
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data processing