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S-nitrosylated blackfin tuna myoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MYT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 293 0.2 M potassium/sodium tartrate, 0.1 M sodium citrate, and 2.0 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 193K, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.943 α = 90 b = 51.932 β = 103.75 c = 38.899 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 RIGAKU SATURN 92 Osmic 2006-05-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.09 30 98.4 0.061 18.1 6.1 54705 51387 8.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.09 1.13 98.4 0.365 3.3 3.5 5466
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 1MYT 1.09 30 51131 2684 98.36 0.13429 0.13317 0.1416 0.15654 0.1656 RANDOM 8.522
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] 0.25 0.06 -0.12 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.041 r_dihedral_angle_4_deg 10.76 r_dihedral_angle_3_deg 10.732 r_dihedral_angle_1_deg 9.043 r_sphericity_free 8.401 r_sphericity_bonded 3.516 r_scangle_it 3.45 r_scbond_it 2.74 r_mcangle_it 1.992 r_mcbond_it 1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.041 r_dihedral_angle_4_deg 10.76 r_dihedral_angle_3_deg 10.732 r_dihedral_angle_1_deg 9.043 r_sphericity_free 8.401 r_sphericity_bonded 3.516 r_scangle_it 3.45 r_scbond_it 2.74 r_mcangle_it 1.992 r_mcbond_it 1.7 r_angle_refined_deg 1.541 r_rigid_bond_restr 1.376 r_angle_other_deg 0.966 r_mcbond_other 0.662 r_nbd_refined 0.237 r_nbtor_refined 0.2 r_nbd_other 0.175 r_xyhbond_nbd_refined 0.166 r_symmetry_vdw_other 0.164 r_symmetry_hbond_refined 0.118 r_symmetry_vdw_refined 0.117 r_nbtor_other 0.089 r_chiral_restr 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1097 Nucleic Acid Atoms Solvent Atoms 198 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement CrystalClear data collection CrystalClear data reduction CrystalClear data scaling PHASER phasing