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Structure of K42Y mutant 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, HANGING DROP 8.5 277 2.7 M ammonium sulfate, 20 mM Tris/HCl, 1 mM EDTA, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.04 39.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.002 α = 90 b = 47.515 β = 90 c = 85.243 γ = 90
Symmetry Space Group P 21 21 21
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 22-ID 1.0000 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.24 94.25 36894 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.24 1.271 65.15
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 1.24 24.39 36894 1935 94.25 0.14318 0.14047 0.1411 0.19468 0.1967 RANDOM 18.493
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] 0.62 -0.46 -0.16
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.647 r_dihedral_angle_2_deg 39.113 r_sphericity_bonded 13.704 r_dihedral_angle_3_deg 13.045 r_dihedral_angle_4_deg 10.787 r_rigid_bond_restr 6.608 r_long_range_B_refined 5.776 r_dihedral_angle_1_deg 5.08 r_scangle_other 4.616 r_long_range_B_other 4.37
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 43.647 r_dihedral_angle_2_deg 39.113 r_sphericity_bonded 13.704 r_dihedral_angle_3_deg 13.045 r_dihedral_angle_4_deg 10.787 r_rigid_bond_restr 6.608 r_long_range_B_refined 5.776 r_dihedral_angle_1_deg 5.08 r_scangle_other 4.616 r_long_range_B_other 4.37 r_scbond_it 4.121 r_scbond_other 4.113 r_angle_other_deg 2.795 r_mcangle_other 2.598 r_mcangle_it 2.521 r_angle_refined_deg 2.43 r_mcbond_it 2.231 r_mcbond_other 2.195 r_chiral_restr 0.186 r_bond_refined_d 0.023 r_gen_planes_refined 0.013 r_gen_planes_other 0.011 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1215 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms 81
Software Software Software Name Purpose MAR345dtb data collection REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling