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Blackfin tuna carbonmonoxy-myoglobin, atomic resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NRL PDB entry 2NRL
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, 2.0 M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.286 α = 90 b = 51.714 β = 105.09 c = 38.633 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 MAR CCD 165 mm 2006-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.92 APS 31-ID
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 0.96 17.36 97.89 0.06 28.04 5.4 75194 73608 2
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 0.96 0.986 89.24 0.504 2.2 4.2
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 RIGID BODY refinement THROUGHOUT PDB entry 2NRL 0.96 17.36 75194 73608 3858 97.89 0.15279 0.15179 0.1477 0.17182 0.1644 RANDOM 8.773
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] -7.19 3.37 4.89 2.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.95 r_dihedral_angle_3_deg 14.043 r_dihedral_angle_4_deg 11.826 r_dihedral_angle_1_deg 5.588 r_scangle_it 3.935 r_scbond_it 2.745 r_mcangle_it 2.231 r_angle_refined_deg 1.581 r_mcbond_it 1.418 r_rigid_bond_restr 1.031
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.95 r_dihedral_angle_3_deg 14.043 r_dihedral_angle_4_deg 11.826 r_dihedral_angle_1_deg 5.588 r_scangle_it 3.935 r_scbond_it 2.745 r_mcangle_it 2.231 r_angle_refined_deg 1.581 r_mcbond_it 1.418 r_rigid_bond_restr 1.031 r_angle_other_deg 0.94 r_mcbond_other 0.499 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1091 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 49
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling