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K4U bound crystal peptide deformylase from Acinetobacter baumanii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8.5 287 0.03 M MgCl2, 0.03 M CaCl2, 15% (v/v) PEGMME, 15% (w/v) PEG 20000, 0.1 M Tris (base)/ Bicine pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.23 44.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.176 α = 90 b = 40.176 β = 90 c = 187.645 γ = 120
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 2017-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97950 PAL/PLS 5C (4A)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.1 50 98.2 0.105 0.129 0.075 21.8 2.8 19227
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 2.1 2.14 100 0.316 0.389 0.225 0.83 2.8
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 6JER 2.11 49.99 18121 1053 98.2 0.2011 0.1971 0.2064 0.2721 0.2818 RANDOM 36.625
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.108 r_dihedral_angle_4_deg 22.099 r_dihedral_angle_3_deg 18.743 r_dihedral_angle_1_deg 6.56 r_angle_refined_deg 1.894 r_angle_other_deg 1.184 r_chiral_restr 0.125 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.108 r_dihedral_angle_4_deg 22.099 r_dihedral_angle_3_deg 18.743 r_dihedral_angle_1_deg 6.56 r_angle_refined_deg 1.894 r_angle_other_deg 1.184 r_chiral_restr 0.125 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2584 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 18
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement HKL-2000 data collection HKL-2000 data reduction MOLREP phasing