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Crystal structure of E. coli YbgJK
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MML
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Reservoir solution: 0.1 M Bicine, pH 8.5, 20% PEG 6000. Protein storage buffer: 20 mM Tris-pH 8.0, 300 mM NaCl, 10% glycerol. Additives: TCEP, malonamide.
Crystal Properties Matthews coefficient Solvent content 2.06 40.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.11 α = 90 b = 88.78 β = 101.91 c = 83.7 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 315r 2008-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.8 15 98.9 0.08 14.43 3.67 23159 71.04
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.88 97.4 0.478 0.557 2.66 3.77
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 3MML 2.8 15 22991 1185 98.62 0.2685 0.2675 0.2961 0.2876 0.3139 RANDOM 48.44
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] 2.078 -3.5418 3.2709 -5.3489
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 3.27 t_omega_torsion 2.51 t_angle_deg 0.95 t_bond_d 0.008 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 3.27 t_omega_torsion 2.51 t_angle_deg 0.95 t_bond_d 0.008 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 14165 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling MR-Rosetta phasing PDB_EXTRACT data extraction