☰ Navigation Tabs
Crystal structure analysis of hellethionin D
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NBL PDB ENTRY 1NBL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 0.1 M sodium iodide, 0.1 M Tris, pH 7.0, 0.2 M magnesium chloride hexahydrate, 1.9 M sodium chloride, protein solution was 45 mg/mL in HEPES diffusion, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.18 61.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.829 α = 90 b = 129.829 β = 90 c = 103.994 γ = 90
Symmetry Space Group I 4 2 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 MARMOSAIC 225 mm CCD 2009-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.9540,1.900 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.95 91.8 99.9 0.1224 0.1224 38.36 45.9 32601 32570 -3 -3 22.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2,3 1.95 2.05 99.9 0.4054 0.4054 38.36 16.75 4446
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MR SAD THROUGHOUT PDB ENTRY 1NBL 1.95 91.8 32601 31827 1622 97.6 0.192 0.19 0.2477 0.221 0.2817 SHELLS 27.52
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] -2.11 -2.11 4.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.758 r_dihedral_angle_4_deg 18.789 r_dihedral_angle_3_deg 10.507 r_dihedral_angle_1_deg 5.237 r_scangle_it 2.026 r_scbond_it 1.301 r_angle_refined_deg 1.131 r_angle_other_deg 0.866 r_mcangle_it 0.756 r_mcbond_it 0.431
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.758 r_dihedral_angle_4_deg 18.789 r_dihedral_angle_3_deg 10.507 r_dihedral_angle_1_deg 5.237 r_scangle_it 2.026 r_scbond_it 1.301 r_angle_refined_deg 1.131 r_angle_other_deg 0.866 r_mcangle_it 0.756 r_mcbond_it 0.431 r_mcbond_other 0.128 r_chiral_restr 0.066 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2322 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 52
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement XDS data reduction SADABS data scaling