1V4U

Crystal structure of bluefin tuna carbonmonoxy-hemoglobin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH METHOD7.5293PEG 2000, sodium phosphate, pH 7.5, BATCH METHOD, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
2.5952.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.016α = 90
b = 102.541β = 90
c = 108.451γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44B21.0000SPring-8BL44B2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
122089.10.0362.940369
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.0764.70.141

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2203827420131000.207330.204390.26429RANDOM30.3
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]
1.87-0.51-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.928
r_scangle_it5.25
r_scbond_it3.597
r_angle_refined_deg2.34
r_mcangle_it2.171
r_mcbond_it1.27
r_symmetry_vdw_refined0.269
r_nbd_refined0.237
r_chiral_restr0.193
r_xyhbond_nbd_refined0.167
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.928
r_scangle_it5.25
r_scbond_it3.597
r_angle_refined_deg2.34
r_mcangle_it2.171
r_mcbond_it1.27
r_symmetry_vdw_refined0.269
r_nbd_refined0.237
r_chiral_restr0.193
r_xyhbond_nbd_refined0.167
r_symmetry_hbond_refined0.085
r_bond_refined_d0.029
r_gen_planes_refined0.011
r_nbd_other
r_nbtor_other
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_gen_planes_other
r_symmetry_vdw_other
r_nbtor_refined
r_symmetry_hbond_other
r_dihedral_angle_4_deg
r_mcbond_other
r_dihedral_angle_3_deg
r_dihedral_angle_2_deg
r_angle_other_deg
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4376
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms180

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing