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Crystal structure of Aedes aegypti Dopachrome Conversion Enzyme with L-Dopamine.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9W1K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 0.1 M Sodium cacodylate trihydrate pH 6.5, 0.2 M Calcium acetate hydrate, and 20% w/v Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.01 38.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.308 α = 90 b = 103.874 β = 110.35 c = 99.034 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 315r 2008-07-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
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 3.39 30 100 0.13 16.2 7.4 23333
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 3.39 3.52 0.372
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 3.39 29.66 22042 1196 99.2 0.19838 0.19431 0.1951 0.27375 0.2729 RANDOM 67.55
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 -0.02 0.02
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 11.91 r_long_range_B_refined 11.908 r_dihedral_angle_3_deg 8.643 r_scangle_other 8.061 r_mcangle_it 7.583 r_mcangle_other 7.583 r_dihedral_angle_2_deg 5.456 r_dihedral_angle_1_deg 4.987 r_scbond_it 4.93 r_scbond_other 4.929
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_other 11.91 r_long_range_B_refined 11.908 r_dihedral_angle_3_deg 8.643 r_scangle_other 8.061 r_mcangle_it 7.583 r_mcangle_other 7.583 r_dihedral_angle_2_deg 5.456 r_dihedral_angle_1_deg 4.987 r_scbond_it 4.93 r_scbond_other 4.929 r_mcbond_it 4.709 r_mcbond_other 4.68 r_angle_other_deg 1.735 r_angle_refined_deg 0.863 r_chiral_restr 0.297 r_gen_planes_other 0.016 r_gen_planes_refined 0.009 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12892 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 343
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling HKL-2000 data reduction MOLREP phasing PDB_EXTRACT data extraction