5AZQ

Crystal structure of cyano-cobalt(III) tetradehydrocorrin in the heme pocket of horse heart myoglobin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.4298ammonium sulfate, Tris-HCl, trehalose
Crystal Properties
Matthews coefficientSolvent content
1.831.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 34.774α = 90
b = 28.808β = 105.64
c = 63.258γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2012-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.90000SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.45097.80.05622.63.6123585
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.4595.52.4

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 DIFFRACTIONTHROUGHOUT1.45022308120097.390.131470.128140.18931RANDOM18.802
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]
0.04-0.661.54-1.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.601
r_sphericity_free30.037
r_dihedral_angle_4_deg20.626
r_dihedral_angle_3_deg13.183
r_sphericity_bonded11.715
r_long_range_B_refined6.987
r_dihedral_angle_1_deg4.745
r_rigid_bond_restr4.474
r_long_range_B_other3.864
r_scangle_other3.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.601
r_sphericity_free30.037
r_dihedral_angle_4_deg20.626
r_dihedral_angle_3_deg13.183
r_sphericity_bonded11.715
r_long_range_B_refined6.987
r_dihedral_angle_1_deg4.745
r_rigid_bond_restr4.474
r_long_range_B_other3.864
r_scangle_other3.56
r_angle_refined_deg3.07
r_scbond_it3.048
r_scbond_other2.992
r_mcangle_it2.254
r_mcangle_other2.253
r_mcbond_it1.872
r_mcbond_other1.852
r_angle_other_deg1.139
r_chiral_restr0.159
r_bond_refined_d0.027
r_gen_planes_refined0.017
r_gen_planes_other0.008
r_bond_other_d0.004
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 AtomsNumber
Protein Atoms1199
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Cootmodel building
PHASERphasing