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THE CRYSTAL STRUCTURE OF A COMPLEX OF Leishmania major DUTPASE WITH SUBSTRATE ANALOGUE DUPNHP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OGK PDB ENTRY 1OGK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 30% PEG 3350 MME, 0.2 M MGCL2, 0.1M BIS-TRIS PH 5.5
Crystal Properties Matthews coefficient Solvent content 2.7 54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.866 α = 90 b = 87.866 β = 90 c = 146.531 γ = 120
Symmetry Space Group P 65 2 2
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 CCD 2004-09-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.34 30 99.9 0.07 28 13.8 14713 3
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) 1 2.34 2.42 99.9 0.43 3.3 8
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 1OGK 2.34 76.03 13849 737 99.2 0.187 0.184 0.1906 0.238 0.2387 RANDOM 50.77
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] 0.01 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.765 r_dihedral_angle_4_deg 19.711 r_dihedral_angle_3_deg 17.212 r_dihedral_angle_1_deg 6.074 r_scangle_it 2.509 r_scbond_it 1.665 r_angle_refined_deg 1.497 r_mcangle_it 1.096 r_angle_other_deg 0.939 r_mcbond_it 0.669
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.765 r_dihedral_angle_4_deg 19.711 r_dihedral_angle_3_deg 17.212 r_dihedral_angle_1_deg 6.074 r_scangle_it 2.509 r_scbond_it 1.665 r_angle_refined_deg 1.497 r_mcangle_it 1.096 r_angle_other_deg 0.939 r_mcbond_it 0.669 r_symmetry_vdw_other 0.294 r_nbd_refined 0.218 r_nbtor_refined 0.185 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.17 r_mcbond_other 0.14 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.096 r_symmetry_vdw_refined 0.092 r_nbtor_other 0.085 r_bond_refined_d 0.015 r_metal_ion_refined 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2000 Nucleic Acid Atoms Solvent Atoms 88 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing