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Wild-type sperm whale myoglobin with nitric oxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MBW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M Tris-Hcl, 1 mM EDTA, pH 7.4
2.56 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 1.84 33.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.8 α = 90 b = 29.26 β = 105.79 c = 63.949 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 IMAGE PLATE RIGAKU RAXIS IV++ 2013-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.7 26.42 80.5 0.03 0.038 0.023 0.999 30.1 2.4 11177
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 80 0.099 0.131 0.083 0.983 2.2
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 2MBW 1.7 26.42 10618 558 80.26 0.1395 0.1368 0.1516 0.1903 0.2005 RANDOM 15.596
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] -0.63 1.05 -0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.65 r_dihedral_angle_4_deg 13.41 r_dihedral_angle_3_deg 12.1 r_dihedral_angle_1_deg 5.561 r_angle_refined_deg 1.999 r_angle_other_deg 1.099 r_chiral_restr 0.144 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.65 r_dihedral_angle_4_deg 13.41 r_dihedral_angle_3_deg 12.1 r_dihedral_angle_1_deg 5.561 r_angle_refined_deg 1.999 r_angle_other_deg 1.099 r_chiral_restr 0.144 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_gen_planes_other 0.007 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1203 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 59
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction