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Coproporphyrinogen III oxidase from Leishmania major
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VJU PDB entry 1VJU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 1 ul Protein 11 mg/ml, 1 ul Crystallization buffer: 35% PEG 5000 MME, 200 mM Ammonium sulfate, 100 mM MES pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.083 α = 86.28 b = 53.808 β = 77.28 c = 65.828 γ = 60.99
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 2006-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97930 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 1.75 46.98 94.6 0.049 15.2 3.3 58682 18.03259
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 1.75 1.81 77 0.229 1.8 4755
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 THROUGHOUT PDB entry 1VJU 1.75 20 58641 2958 94.42 0.166 0.165 0.1747 0.193 0.198 RANDOM 12.392
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] -0.21 -0.27 0.52 0.27 0.12 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.256 r_dihedral_angle_4_deg 12.353 r_dihedral_angle_3_deg 12.045 r_dihedral_angle_1_deg 5.332 r_scangle_it 1.441 r_angle_other_deg 1.194 r_angle_refined_deg 1.027 r_scbond_it 0.96 r_mcangle_it 0.65 r_mcbond_it 0.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.256 r_dihedral_angle_4_deg 12.353 r_dihedral_angle_3_deg 12.045 r_dihedral_angle_1_deg 5.332 r_scangle_it 1.441 r_angle_other_deg 1.194 r_angle_refined_deg 1.027 r_scbond_it 0.96 r_mcangle_it 0.65 r_mcbond_it 0.458 r_symmetry_vdw_other 0.225 r_nbd_refined 0.189 r_nbtor_refined 0.184 r_nbd_other 0.179 r_symmetry_vdw_refined 0.148 r_symmetry_hbond_refined 0.106 r_xyhbond_nbd_refined 0.104 r_nbtor_other 0.084 r_mcbond_other 0.078 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4875 Nucleic Acid Atoms Solvent Atoms 532 Heterogen Atoms 12
Software Software Software Name Purpose TRUNCATE data reduction DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction MAR345 data collection REFMAC refinement