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Structure and activity of human mitochondrial peptide deformylase, a novel cancer target
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 5.6 277 1 M AMMONIUM PHOSPHATE MONOBASIC, 0,1 M SODIUM CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.89 57.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.332 α = 90 b = 77.825 β = 107.93 c = 111.041 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 ADSC QUANTUM 315 2006-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-C 0.97922 APS 24-ID-C
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 1.7 100 100 0.061 5.2 99992 5
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 1.7 1.76 100 0.38 5.1 5.1
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 1ZXZ 1.7 37.53 100609 97531 5136 99.64 0.16241 0.16111 0.1631 0.18697 0.1898 RANDOM 18.009
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] 0.25 -0.25 -0.26 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.961 r_dihedral_angle_4_deg 18.089 r_dihedral_angle_3_deg 14.203 r_scangle_it 6.672 r_dihedral_angle_1_deg 5.94 r_scbond_it 4.15 r_mcangle_it 2.736 r_angle_refined_deg 2.239 r_mcbond_it 1.508 r_chiral_restr 0.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.961 r_dihedral_angle_4_deg 18.089 r_dihedral_angle_3_deg 14.203 r_scangle_it 6.672 r_dihedral_angle_1_deg 5.94 r_scbond_it 4.15 r_mcangle_it 2.736 r_angle_refined_deg 2.239 r_mcbond_it 1.508 r_chiral_restr 0.196 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 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 5780 Nucleic Acid Atoms Solvent Atoms 715 Heterogen Atoms 44
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling