☰ Navigation Tabs
Crystal structure of a human-like mitochondrial peptide deformylase in complex with Met-Ala-Ser
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZXZ PDB entry 1ZXZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 5-15% PEG 5000 MME, 100mM MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.55 α = 90 b = 74.71 β = 90 c = 109.76 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 2009-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50 99.5 0.084 11.68 4.2 16326 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.54 97.2 0.386 3.03 4.2
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 THROUGHOUT PDB entry 1ZXZ 2.4 46.68 16326 860 100 0.17761 0.17381 0.1911 0.25096 0.2553 RANDOM 44.227
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] -2.15 4.83 -2.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.475 r_dihedral_angle_3_deg 18.82 r_dihedral_angle_4_deg 16.578 r_dihedral_angle_1_deg 7.765 r_scangle_it 4.896 r_scbond_it 3.337 r_angle_refined_deg 2.667 r_mcangle_it 1.799 r_mcbond_it 1.277 r_metal_ion_refined 0.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.475 r_dihedral_angle_3_deg 18.82 r_dihedral_angle_4_deg 16.578 r_dihedral_angle_1_deg 7.765 r_scangle_it 4.896 r_scbond_it 3.337 r_angle_refined_deg 2.667 r_mcangle_it 1.799 r_mcbond_it 1.277 r_metal_ion_refined 0.373 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.293 r_symmetry_vdw_refined 0.231 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.183 r_chiral_restr 0.143 r_bond_refined_d 0.03 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other 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 3005 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling REFMAC phasing