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Crystal structure of E.coli CcdB mutant V46L
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, 25% PEG 3350
Crystal Properties Matthews coefficient Solvent content 1.92 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.1 α = 90 b = 36.76 β = 115.19 c = 35.91 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 PIXEL DECTRIS PILATUS 6M 2021-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0358 ELETTRA 11.2C
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 1.35 33.98 100 0.098 0.108 0.043 0.994 11.6 5.9 19433 5.8
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 1.35 1.43 100 0.288 0.322 0.141 0.928 3.7 5.1
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 1.354 33.979 19429 855 99.979 0.163 0.1616 0.1618 0.1844 0.1844 9.358
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] 0.031 -0.123 0.276 -0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.249 r_dihedral_angle_4_deg 23.625 r_dihedral_angle_3_deg 13.47 r_dihedral_angle_1_deg 6.444 r_lrange_it 4.686 r_lrange_other 4.385 r_scangle_it 2.351 r_scangle_other 2.349 r_angle_refined_deg 1.922 r_mcangle_other 1.887
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.249 r_dihedral_angle_4_deg 23.625 r_dihedral_angle_3_deg 13.47 r_dihedral_angle_1_deg 6.444 r_lrange_it 4.686 r_lrange_other 4.385 r_scangle_it 2.351 r_scangle_other 2.349 r_angle_refined_deg 1.922 r_mcangle_other 1.887 r_mcangle_it 1.884 r_scbond_it 1.547 r_scbond_other 1.547 r_angle_other_deg 1.515 r_mcbond_it 1.227 r_mcbond_other 1.223 r_symmetry_nbd_refined 0.377 r_symmetry_xyhbond_nbd_refined 0.3 r_nbd_other 0.258 r_xyhbond_nbd_refined 0.253 r_nbd_refined 0.208 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.169 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.093 r_symmetry_xyhbond_nbd_other 0.086 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 167 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing