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Yersinia YscU C-terminal fragment in complex with a synthetic compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.8 M potassium dihydrogen phosphate, 0.8 M disodium hydrogen phosphate, 0.1 M Hepes
Crystal Properties Matthews coefficient Solvent content 3.27 62.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.74 α = 90 b = 69.65 β = 90 c = 242.67 γ = 90
Symmetry Space Group I 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 PILATUS3 X 2M 2014-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87290 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.48 44.8 99.7 0.121 0.99 15.1 13.3 16706 68.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.48 2.63 98.6 0.877 0.9 14
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2JLI 2.48 23.39 16636 832 99.9 0.2162 0.2144 0.2522 0.2411 RANDOM 68.06
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] -15.9696 -2.0355 18.0051
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.54 t_omega_torsion 3.44 t_angle_deg 1.2 t_bond_d 0.012 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.54 t_omega_torsion 3.44 t_angle_deg 1.2 t_bond_d 0.012 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 2324 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 51
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling BALBES phasing