☰ Navigation Tabs
Crystal structure of putative melanin biosynthesis protein TyrA with bound heme (NP_716371.1) from Shewanella Oneidensis at 2.30 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 287 0.1M Tris, 5% isopropyl alcohol, 20% (w/v) polyethylene glycol 4000, additive - 1mM hemin, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K
Crystal Properties Matthews coefficient Solvent content 3.58 65.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.837 α = 90 b = 94.837 β = 90 c = 116.666 γ = 90
Symmetry Space Group P 43 21 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 QUANTUM 315 Flat mirror (vertical focusing) 2006-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 2.3 19.9 99.7 0.142 11.72 6.95 24210 38.592
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 2.3 2.45 100 0.552 3 4094
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 2HAG 2.3 19.8 24207 1269 99.88 0.208 0.205 0.2097 0.266 0.2686 RANDOM 33.304
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] -1.39 -1.39 2.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.049 r_dihedral_angle_4_deg 16.274 r_dihedral_angle_3_deg 13.869 r_dihedral_angle_1_deg 6.456 r_scangle_it 5.78 r_scbond_it 4.387 r_mcangle_it 2.281 r_angle_refined_deg 1.357 r_mcbond_it 1.33 r_angle_other_deg 0.763
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.049 r_dihedral_angle_4_deg 16.274 r_dihedral_angle_3_deg 13.869 r_dihedral_angle_1_deg 6.456 r_scangle_it 5.78 r_scbond_it 4.387 r_mcangle_it 2.281 r_angle_refined_deg 1.357 r_mcbond_it 1.33 r_angle_other_deg 0.763 r_mcbond_other 0.329 r_symmetry_hbond_refined 0.292 r_symmetry_vdw_refined 0.255 r_symmetry_vdw_other 0.24 r_nbd_refined 0.203 r_nbd_other 0.19 r_nbtor_refined 0.18 r_xyhbond_nbd_refined 0.134 r_nbtor_other 0.087 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_bond_other_d 0.002 r_gen_planes_refined 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2441 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 56
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement MolProbity model building PDB_EXTRACT data extraction XDS data reduction