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K1U bound crystal structure of class I type b peptide deformylase from Pseudomonas aeruginosa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JF9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 8 287 0.03M CaCl2, 0.03M MgCl2, 0.1M Sodium Hepes, MOPS pH 8.0, 10.0%(v/v) MPD, 10.0%(w/v) P1k, 10.0%(w/v) PEG 3,350
Crystal Properties Matthews coefficient Solvent content 2.77 55.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.33 α = 90 b = 146.356 β = 109.9 c = 65.306 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 2017-06-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97960 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 2.4 50 95.1 0.104 0.117 0.052 11.8 4.1 29213
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 2.4 2.44 89.4 0.446 0.54 0.296 0.245 2.6
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 6JF9 2.4 49.99 27592 1489 95.13 0.2282 0.2251 0.2276 0.2835 0.2839 RANDOM 40.249
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] 0.01 -0.01 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.733 r_dihedral_angle_3_deg 18.075 r_dihedral_angle_4_deg 15.756 r_dihedral_angle_1_deg 6.94 r_angle_refined_deg 1.692 r_angle_other_deg 1.029 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.733 r_dihedral_angle_3_deg 18.075 r_dihedral_angle_4_deg 15.756 r_dihedral_angle_1_deg 6.94 r_angle_refined_deg 1.692 r_angle_other_deg 1.029 r_chiral_restr 0.093 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5048 Nucleic Acid Atoms Solvent Atoms 22 Heterogen Atoms 30
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement HKL-2000 data collection HKL-2000 data reduction MOLREP phasing