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Plasmodium falciparum peptide deformylase complex with inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JYM PDB ENTRY 1JYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 294 sodium monobasic phosphate, potassium dibasic phosphate, lithium sulfate, CAPS, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 4.01 69.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.317 α = 90 b = 102.317 β = 90 c = 118.339 γ = 120
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 2002-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.98 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 2.18 41.6 99.9 0.111 11.4 6.3 36742 -3 33.9
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 2.18 2.3 100 0.714 2.6 6.3 5325
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 (All) 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 1JYM 2.18 20 36594 36594 1811 99.99 0.19806 0.19806 0.1973 0.2085 0.2122 0.2293 RANDOM 39.587
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]
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.397 r_dihedral_angle_1_deg 5.872 r_scbond_it 5.727 r_mcangle_it 4.314 r_mcbond_it 2.442 r_angle_refined_deg 1.313 r_symmetry_hbond_refined 0.304 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.219 r_symmetry_vdw_refined 0.185
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.397 r_dihedral_angle_1_deg 5.872 r_scbond_it 5.727 r_mcangle_it 4.314 r_mcbond_it 2.442 r_angle_refined_deg 1.313 r_symmetry_hbond_refined 0.304 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.219 r_symmetry_vdw_refined 0.185 r_chiral_restr 0.096 r_metal_ion_refined 0.014 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2555 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing