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The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G27 PDB entry 1G27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 294 20% PEG3350, 0.2M Potassium formate, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.84 56.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.96 α = 90 b = 73.96 β = 90 c = 241.5 γ = 90
Symmetry Space Group P 43 2 2
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 315 Si (111) double crystal monochromator. Kirkpatrick Baez bimorph mirror pair for horizontal and vertical focussing 2009-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.15 241.5 90.8 0.069 0.064 8.4 7.5 37679 1.6 36.6
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 PDB entry 1G27 2.15 241.5 32520 1690 90.79 0.26113 0.2582 0.2513 0.31919 0.3086 RANDOM 47.589
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] -0.74 -0.74 1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.358 r_dihedral_angle_4_deg 17.258 r_dihedral_angle_3_deg 16.148 r_dihedral_angle_1_deg 5.396 r_scangle_it 2.266 r_scbond_it 1.294 r_angle_refined_deg 1.162 r_mcangle_it 1.097 r_mcbond_it 0.594 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.358 r_dihedral_angle_4_deg 17.258 r_dihedral_angle_3_deg 16.148 r_dihedral_angle_1_deg 5.396 r_scangle_it 2.266 r_scbond_it 1.294 r_angle_refined_deg 1.162 r_mcangle_it 1.097 r_mcbond_it 0.594 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3854 Nucleic Acid Atoms Solvent Atoms 233 Heterogen Atoms 51
Software Software Software Name Purpose DNA data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling