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Crystal structure of peptide deformylase from ehrlichia chaffeensis in complex with actinonin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OCA PDB entry 3oca, native EhchA.01519.a
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 290 EBS SCREEN JCSG+ A9: 15-20% PEG 3350, 200MM AMMONIUM CHLORIDE; EHCHA.01519.A.A1.PW27438 AT 14MG/ML, CRYO PROTECTED WITH AL'S OIL, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties Matthews coefficient Solvent content 2.17 43.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.89 α = 90 b = 33.02 β = 91.17 c = 68.14 γ = 90
Symmetry Space Group C 1 2 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 RIGAKU SATURN 944+ RIGAKU VARIMAX HF 2011-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF
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 1.7 41.936 97.8 0.031 20920 20709 -3 25.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 80.9 0.188 5.19
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3oca, native EhchA.01519.a 1.7 41.936 20709 20709 1062 0.172 0.17 0.1781 0.198 0.2051 RANDOM 23.09
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] -0.78 0.23 1.67 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.18 r_dihedral_angle_4_deg 19.61 r_dihedral_angle_3_deg 12.31 r_dihedral_angle_1_deg 5.7 r_angle_refined_deg 1.555 r_angle_other_deg 0.941 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.18 r_dihedral_angle_4_deg 19.61 r_dihedral_angle_3_deg 12.31 r_dihedral_angle_1_deg 5.7 r_angle_refined_deg 1.555 r_angle_other_deg 0.941 r_chiral_restr 0.094 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1329 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 30
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement