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Leishmania major coproporphyrinogen III oxidase with bound ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QT8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 295 200mM ammonium sulfate, 29% PEG 5000MME, 100 mM MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.16 43.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.487 α = 90 b = 48.06 β = 90.06 c = 84.442 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 MARMOSAIC 325 mm CCD 2006-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03322 APS 23-ID-B
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 1.66 50 88.3 0.038 21.7 3.6 63608
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 1.66 1.72 41.3 0.267 1.8
Refinement Statistics Diffraction ID Structure Solution 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) Mean Isotropic B X-RAY DIFFRACTION 2QT8 1.66 50 63544 3145 88.3 0.164 0.163 0.1762 0.186 0.1947 17.01
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] 0.36 0.1 -0.13 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.641 r_dihedral_angle_4_deg 17.621 r_dihedral_angle_3_deg 12.986 r_dihedral_angle_1_deg 5.442 r_scangle_it 2.767 r_scbond_it 1.711 r_angle_refined_deg 1.224 r_mcangle_it 1.037 r_angle_other_deg 0.833 r_mcbond_it 0.558
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.641 r_dihedral_angle_4_deg 17.621 r_dihedral_angle_3_deg 12.986 r_dihedral_angle_1_deg 5.442 r_scangle_it 2.767 r_scbond_it 1.711 r_angle_refined_deg 1.224 r_mcangle_it 1.037 r_angle_other_deg 0.833 r_mcbond_it 0.558 r_mcbond_other 0.151 r_chiral_restr 0.074 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4558 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 74
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction