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F33Y CuB myoglobin (F33Y L29H F43H sperm whale myoglobin) with copper bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 F33Y-CuBMb (1.0 mM) in 100 mM tris pH 8, (pH adjusted H2SO4), was mixed 1:3 with well buffer (0.1 M sodium cacodylate pH 6.5, 0.2 M sodium acetate trihydrate with 30% w/v polyethylene glycol 8000) using the hanging drop method with 300 uL well buffer in the well of the crystallization tray. Crystals obtained by this method were soaked with 10 eq CuSO4 in a mixture of E-F33Y CuBMb and well buffer consistent with the original drop conditions to avoid dissolving the crystals and subsequently with 15eq potassium cyanide, in a mixture of E-F33Y-CuBMb and well buffer using pH 7.0 sodium cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.16 43.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.734 α = 90 b = 48.286 β = 90 c = 77.691 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 77 CCD ADSC QUANTUM 315 2011-08-18 M SINGLE WAVELENGTH 2 1 x-ray 77 CCD ADSC QUANTUM 315 2011-08-18 M SINGLE WAVELENGTH 3 1 x-ray 77 CCD ADSC QUANTUM 315 2011-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A 2 SYNCHROTRON NSLS BEAMLINE X29A 1.388 NSLS X29A 3 SYNCHROTRON NSLS BEAMLINE X29A 1.372 NSLS X29A
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 1,2,3 1.8 50 100 0.111 23.3 14457 14457
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) 1,2,3 1.8 1.86 100 0.637 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 4FWZ 1.8 41.01 13729 13729 727 99.74 0.20079 0.20079 0.1985 0.1973 0.24619 0.2425 RANDOM 34.604
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] -0.82 0.2 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.117 r_dihedral_angle_4_deg 23.254 r_dihedral_angle_3_deg 17.018 r_dihedral_angle_1_deg 5.396 r_angle_refined_deg 3.188 r_chiral_restr 0.206 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.117 r_dihedral_angle_4_deg 23.254 r_dihedral_angle_3_deg 17.018 r_dihedral_angle_1_deg 5.396 r_angle_refined_deg 3.188 r_chiral_restr 0.206 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1219 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 48
Software Software Software Name Purpose CBASS data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling