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Crystal structure of E.coli CcdB mutant S12G
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 0.15 M CaCl2.2H2O, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.87 34.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.57 α = 90 b = 36.53 β = 93.691 c = 67.528 γ = 90
Symmetry Space Group I 1 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 IMAGE PLATE RIGAKU RAXIS IV++ 2019-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-X 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.63 33.69 90.6 0.083 0.093 0.041 0.995 9.8 4.9 9822 11.66
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.63 1.72 86.9 0.195 0.218 0.097 0.967 4.8 4.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3VUB 1.631 33.69 9822 455 89.92 0.23 0.2276 0.2347 0.2694 0.2796 0 17.012
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] -0.381 0.446 0.702 -0.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.127 r_dihedral_angle_4_deg 17.491 r_dihedral_angle_3_deg 14.173 r_dihedral_angle_1_deg 6.288 r_lrange_it 4.629 r_lrange_other 4.497 r_scangle_it 2.294 r_scangle_other 2.293 r_mcangle_it 2.263 r_mcangle_other 2.245
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.127 r_dihedral_angle_4_deg 17.491 r_dihedral_angle_3_deg 14.173 r_dihedral_angle_1_deg 6.288 r_lrange_it 4.629 r_lrange_other 4.497 r_scangle_it 2.294 r_scangle_other 2.293 r_mcangle_it 2.263 r_mcangle_other 2.245 r_angle_refined_deg 1.484 r_mcbond_it 1.416 r_scbond_it 1.403 r_scbond_other 1.401 r_mcbond_other 1.385 r_angle_other_deg 1.253 r_symmetry_nbd_refined 0.266 r_nbd_other 0.256 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.183 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.117 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 792 Nucleic Acid Atoms Solvent Atoms 95 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing