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Blackfin tuna myoglobin imidazole complex, 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 2.19 43.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.198 α = 90 b = 52.381 β = 104.43 c = 39.022 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 0.94 16.78 97.54 0.065 27.4 5.3 81961 79945 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 0.94 0.965 88.35 0.469 2.32 4
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 0.94 16.78 81961 79945 4204 97.54 0.1471 0.1464 0.1407 0.16039 0.1559 RANDOM 7.916
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] -3.98 -1.87 4.62 -0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.573 r_dihedral_angle_4_deg 14.419 r_dihedral_angle_3_deg 13.938 r_dihedral_angle_1_deg 4.567 r_scangle_it 3.953 r_scbond_it 2.742 r_mcangle_it 2.101 r_angle_refined_deg 1.602 r_mcbond_it 1.327 r_rigid_bond_restr 0.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.573 r_dihedral_angle_4_deg 14.419 r_dihedral_angle_3_deg 13.938 r_dihedral_angle_1_deg 4.567 r_scangle_it 3.953 r_scbond_it 2.742 r_mcangle_it 2.101 r_angle_refined_deg 1.602 r_mcbond_it 1.327 r_rigid_bond_restr 0.992 r_angle_other_deg 0.968 r_mcbond_other 0.481 r_chiral_restr 0.085 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 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 197 Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection REFMAC refinement DENZO data reduction SCALEPACK data scaling