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Coproporphyrinogen III oxidase from Leishmania naiffi
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 5.5 277 0.1 M ammonium acetate (not pH'ed), 0.1 M bis-tris (pH 5.5), 21% PEG 10K, 5 mM DTT; cryoprotected with 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.71 54.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.097 α = 90 b = 73.147 β = 90 c = 184.745 γ = 90
Symmetry Space Group P 21 21 21
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 315 Vertical focusing mirror; single crystal Si(311) bent monochromator (horizontal focusing) 2008-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.9795 SSRL BL9-1
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 2.27 50 97 0.057 6.7 34890 1 38.6
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 2.27 2.35 87.1 0.263 6.7 3092
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 2qt8 2.27 50 34744 1735 96.68 0.191 0.188 0.2151 0.245 0.2635 RANDOM 27.895
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] 3.54 -0.65 -2.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.81 r_dihedral_angle_3_deg 14.035 r_dihedral_angle_4_deg 12.86 r_dihedral_angle_1_deg 5.094 r_scangle_it 3.743 r_scbond_it 2.571 r_mcangle_it 2.098 r_mcbond_it 1.272 r_angle_refined_deg 1.019 r_angle_other_deg 0.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.81 r_dihedral_angle_3_deg 14.035 r_dihedral_angle_4_deg 12.86 r_dihedral_angle_1_deg 5.094 r_scangle_it 3.743 r_scbond_it 2.571 r_mcangle_it 2.098 r_mcbond_it 1.272 r_angle_refined_deg 1.019 r_angle_other_deg 0.993 r_mcbond_other 0.349 r_chiral_restr 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4654 Nucleic Acid Atoms Solvent Atoms 307 Heterogen Atoms 38
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection HKL-2000 data reduction HKL-2000 data scaling