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Structure of K42N variant of sperm whale myoglobin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OCK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 277 2.7 M ammonium sulfate, 20 mM Tris, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.1 60.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.304 α = 90 b = 90.304 β = 90 c = 45.314 γ = 120
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 300 mm CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.00000 APS 21-ID-D
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 1.241 24.76 98.6 0.058 36.1 5.8 58965 1
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 1.241 1.273 90.4 0.209 2.1 3753
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 3OCK 1.241 24.76 55979 2983 98.76 0.11969 0.11854 0.1182 0.14123 0.1389 RANDOM 11.499
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] 0.08 0.08 0.08 -0.25
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 52.813 r_dihedral_angle_2_deg 36.66 r_dihedral_angle_3_deg 13.116 r_sphericity_bonded 9.93 r_rigid_bond_restr 8.353 r_dihedral_angle_4_deg 5.437 r_dihedral_angle_1_deg 5.192 r_long_range_B_refined 4.706 r_long_range_B_other 3.202 r_angle_refined_deg 2.77
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 52.813 r_dihedral_angle_2_deg 36.66 r_dihedral_angle_3_deg 13.116 r_sphericity_bonded 9.93 r_rigid_bond_restr 8.353 r_dihedral_angle_4_deg 5.437 r_dihedral_angle_1_deg 5.192 r_long_range_B_refined 4.706 r_long_range_B_other 3.202 r_angle_refined_deg 2.77 r_scangle_other 2.334 r_scbond_it 2.27 r_scbond_other 2.255 r_mcangle_it 1.814 r_mcangle_other 1.814 r_mcbond_it 1.347 r_mcbond_other 1.347 r_angle_other_deg 1.152 r_chiral_restr 0.19 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_gen_planes_other 0.01 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1216 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 75
Software Software Software Name Purpose AMoRE phasing REFMAC refinement HKL-3000 data reduction SCALEPACK data scaling