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Crystal structure of the Vibrio cholerae replicative helicase (DnaB) with GDP-AlF4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6QEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291 10% (v/v) MPD
0.1 M MES pH 6.0
Crystal Properties Matthews coefficient Solvent content 3.25 62.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.978 α = 90 b = 123.292 β = 90 c = 263.493 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 PIXEL DECTRIS EIGER X 9M KB Mirrors 2019-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
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 3.9 49.63 99.8 0.226 0.293 0.055 0.997 6.2 18.3 38678 147.24
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.9 4.07 97.7 3.86 1.009 0.314 15.5
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 6QEL 3.9 49.63 27099 1373 75.2 0.256 0.255 0.2694 0.276 0.2965 RANDOM 199.03
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] 6.1779 -5.2436 -0.9344
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.71 t_omega_torsion 1.53 t_angle_deg 0.94 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 21.71 t_omega_torsion 1.53 t_angle_deg 0.94 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20618 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 204
Software Software Software Name Purpose BUSTER refinement XDS data reduction XDS data scaling MOLREP phasing