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Sperm whale myoglobin H64Q 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 9
2.5 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 3.08 60.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.132 α = 90 b = 90.132 β = 90 c = 45.248 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 PIXEL DECTRIS PILATUS 200K 2013-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.78 50 99.3 0.054 0.058 0.021 32.6 7 20200
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 1.78 1.81 86.9 0.084 0.096 0.044 0.989 4.3
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 1.78 31.95 19105 1026 99.52 0.1546 0.1525 0.1649 0.1928 0.202 RANDOM 18.933
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] 0.04 0.04 0.04 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.58 r_dihedral_angle_4_deg 23.217 r_dihedral_angle_3_deg 13.924 r_dihedral_angle_1_deg 5.185 r_angle_refined_deg 2.443 r_mcangle_it 2.336 r_mcbond_it 1.906 r_mcbond_other 1.782 r_angle_other_deg 0.995 r_chiral_restr 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.58 r_dihedral_angle_4_deg 23.217 r_dihedral_angle_3_deg 13.924 r_dihedral_angle_1_deg 5.185 r_angle_refined_deg 2.443 r_mcangle_it 2.336 r_mcbond_it 1.906 r_mcbond_other 1.782 r_angle_other_deg 0.995 r_chiral_restr 0.15 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1216 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 99
Software Software Software Name Purpose HKL-2000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction