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Crystal structure of the WbkC N-formyltransferase (F142A variant) from Brucella melitensis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5VYR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 13-15% PEG5000, 2% glycerol, 5 mM GDP-perosamine, 5 mM folinic acid, 100 mM MES
Crystal Properties Matthews coefficient Solvent content 2.31 46.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.315 α = 90 b = 68.021 β = 90 c = 236.035 γ = 90
Symmetry Space Group P 21 21 21
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 Bruker Platinum 135 montel 2016-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 2.2 50 96.5 0.093 0.093 7.1 6.3 54309
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 80.6 0.412 0.412 1.8 2.2
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 5vyr 2.2 50 51622 2687 96.56 0.20537 0.20213 0.2088 0.26779 0.2717 RANDOM 28.907
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] -0.06 0.44 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.202 r_dihedral_angle_4_deg 16.666 r_dihedral_angle_3_deg 16.316 r_dihedral_angle_1_deg 6.639 r_long_range_B_refined 5.135 r_long_range_B_other 5.114 r_scangle_other 3.488 r_mcangle_it 2.998 r_mcangle_other 2.997 r_scbond_it 2.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.202 r_dihedral_angle_4_deg 16.666 r_dihedral_angle_3_deg 16.316 r_dihedral_angle_1_deg 6.639 r_long_range_B_refined 5.135 r_long_range_B_other 5.114 r_scangle_other 3.488 r_mcangle_it 2.998 r_mcangle_other 2.997 r_scbond_it 2.181 r_scbond_other 2.178 r_mcbond_it 1.863 r_mcbond_other 1.857 r_angle_refined_deg 1.664 r_angle_other_deg 0.992 r_chiral_restr 0.086 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7950 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 194
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing