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Wild-type sperm whale myoglobin with a Fe-phenyl moiety
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 7.4 293 0.1 M Tris-HCl, pH 7.4, 1mM EDTA, 2.5 M Ammonium Sulfate
Crystal Properties Matthews coefficient Solvent content 1.9 35.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.484 α = 90 b = 30.152 β = 105.16 c = 64.463 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 PIXEL DECTRIS PILATUS 200K mirrors 2014-07-24 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) 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 1.87 50 97.1 0.032 18.7 3.6 10468
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 1.87 1.9 92.2 0.309 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 1.87 33.28 9987 476 96.29 0.2156 0.2129 0.2157 0.2781 0.282 RANDOM 20.191
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] 0.34 -0.1 -0.58 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.283 r_dihedral_angle_4_deg 32.78 r_dihedral_angle_3_deg 15.271 r_dihedral_angle_1_deg 5.302 r_angle_refined_deg 1.631 r_mcangle_it 1.278 r_angle_other_deg 1.004 r_mcbond_it 0.748 r_mcbond_other 0.74 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.283 r_dihedral_angle_4_deg 32.78 r_dihedral_angle_3_deg 15.271 r_dihedral_angle_1_deg 5.302 r_angle_refined_deg 1.631 r_mcangle_it 1.278 r_angle_other_deg 1.004 r_mcbond_it 0.748 r_mcbond_other 0.74 r_chiral_restr 0.085 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1203 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms 60
Software Software Software Name Purpose HKL-3000 data collection HKL-3000 data reduction HKL-3000 phasing HKL-3000 data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction