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Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DFF PDB ENTRY 1DFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 Tris, Sodium chloride, Magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.263 α = 90 b = 121.263 β = 90 c = 177.272 γ = 90
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 4 2001-05-05 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97918, 0.97938, 0.96396 ALS 5.0.2
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 2.8 30 99.6 0.101 4.9 62948 51866 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) 2.8 2.9 97.1 0.594
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT PDB ENTRY 1DFF 2.8 30 2 51866 49234 2632 82.49 0.23395 0.2339 0.23062 0.29599 RANDOM 49.586
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] -4.64 -4.64 9.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 24.593 r_scangle_it 8.416 r_scbond_it 5.847 r_mcangle_it 5.644 r_dihedral_angle_1_deg 4.775 r_mcbond_it 3.297 r_angle_refined_deg 1.686 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.163
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 24.593 r_scangle_it 8.416 r_scbond_it 5.847 r_mcangle_it 5.644 r_dihedral_angle_1_deg 4.775 r_mcbond_it 3.297 r_angle_refined_deg 1.686 r_symmetry_hbond_refined 0.276 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.163 r_symmetry_vdw_refined 0.147 r_chiral_restr 0.136 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14397 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 20
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing REFMAC refinement