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Crystal structure of E.coli CcdB mutant S60E
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 5.1 291 200mM CaCl2, 10% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.9 35.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.81 α = 90 b = 36.64 β = 114.97 c = 35.67 γ = 90
Symmetry Space Group C 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 MAR scanner 345 mm plate 2020-12-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 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 1.93 10 97.5 0.13 0.154 0.081 0.99 9.6 3.4 6557 8.6
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 1.93 2.03 91.6 0.424 0.504 0.268 0.801 3.8 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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3VUB 1.931 9.996 6557 333 97.807 0.172 0.1697 0.1797 0.2135 0.2286 10.319
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] -0.006 -0.372 0.359 -0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.936 r_dihedral_angle_4_deg 17.731 r_dihedral_angle_3_deg 14.584 r_dihedral_angle_1_deg 6.452 r_lrange_it 3.335 r_lrange_other 3.117 r_mcangle_other 1.363 r_mcangle_it 1.357 r_angle_refined_deg 1.325 r_scangle_it 1.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.936 r_dihedral_angle_4_deg 17.731 r_dihedral_angle_3_deg 14.584 r_dihedral_angle_1_deg 6.452 r_lrange_it 3.335 r_lrange_other 3.117 r_mcangle_other 1.363 r_mcangle_it 1.357 r_angle_refined_deg 1.325 r_scangle_it 1.216 r_scangle_other 1.216 r_angle_other_deg 1.157 r_mcbond_it 0.756 r_mcbond_other 0.718 r_scbond_it 0.702 r_scbond_other 0.69 r_symmetry_nbd_refined 0.262 r_nbd_other 0.213 r_nbd_refined 0.187 r_symmetry_nbd_other 0.172 r_xyhbond_nbd_refined 0.164 r_nbtor_refined 0.154 r_symmetry_xyhbond_nbd_refined 0.152 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 803 Nucleic Acid Atoms Solvent Atoms 98 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing