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Selective screening and design to identify inhibitors of leishmania major pteridine reductase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E92 PDB ENTRY 1E92
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 12% PEG 5000, 100MM SODIUM ACETATE, 100MM CALCIUM ACETATE, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.8 55.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.206 α = 90 b = 103.492 β = 108.24 c = 146.476 γ = 90
Symmetry Space Group P 1 21 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 4 MIRRORS 2003-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.4 30 95.5 0.25 0.12 8.1 2.7 100504 2 27
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 89.5 0.609 3.1
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 PDB ENTRY 1E92 2.4 30 100504 4985 95.2 0.28 0.276 0.277 0.356 0.3543 RANDOM 23.68
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] -0.38 -0.39 -0.08 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.928 r_dihedral_angle_4_deg 20.789 r_dihedral_angle_3_deg 17.559 r_dihedral_angle_1_deg 7.942 r_scangle_it 7.7 r_scbond_it 6.772 r_mcangle_it 5.108 r_mcbond_it 3.27 r_angle_refined_deg 1.852 r_symmetry_hbond_refined 0.495
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.928 r_dihedral_angle_4_deg 20.789 r_dihedral_angle_3_deg 17.559 r_dihedral_angle_1_deg 7.942 r_scangle_it 7.7 r_scbond_it 6.772 r_mcangle_it 5.108 r_mcbond_it 3.27 r_angle_refined_deg 1.852 r_symmetry_hbond_refined 0.495 r_nbtor_refined 0.315 r_symmetry_vdw_refined 0.307 r_nbd_refined 0.258 r_xyhbond_nbd_refined 0.248 r_chiral_restr 0.117 r_bond_refined_d 0.019 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_metal_ion_refined 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 15900 Nucleic Acid Atoms Solvent Atoms 1098 Heterogen Atoms 640
Software Software Software Name Purpose AMoRE phasing REFMAC refinement HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling