5C6Y

A sperm whale myoglobin double mutant L29H/F43Y Mb with a Tyr-heme cross-link


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4QAU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52930.2 M Sodium acetate trihydrate,0.1 M Sodium cacodylate trihydrate pH 6.5,30% w/v Polyethylene glycol 8000
Crystal Properties
Matthews coefficientSolvent content
2.244.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.062α = 90
b = 48.348β = 90
c = 79.141γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2015-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.988SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.7935099.719.81314678
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)
11.7931.831000.52412.912.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT4QAU1.79341.261388974597.570.157960.156770.18083RANDOM22.367
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]
-1.170.180.99
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.535
r_dihedral_angle_4_deg29.185
r_dihedral_angle_3_deg11.65
r_long_range_B_refined7.937
r_long_range_B_other7.707
r_scangle_other6.351
r_dihedral_angle_1_deg5.047
r_scbond_other4.208
r_scbond_it4.204
r_mcangle_other2.843
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.535
r_dihedral_angle_4_deg29.185
r_dihedral_angle_3_deg11.65
r_long_range_B_refined7.937
r_long_range_B_other7.707
r_scangle_other6.351
r_dihedral_angle_1_deg5.047
r_scbond_other4.208
r_scbond_it4.204
r_mcangle_other2.843
r_mcangle_it2.84
r_angle_refined_deg2.228
r_mcbond_it2.095
r_mcbond_other2.026
r_angle_other_deg1.482
r_chiral_restr0.185
r_bond_refined_d0.026
r_gen_planes_refined0.014
r_gen_planes_other0.007
r_bond_other_d0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1213
Nucleic Acid Atoms
Solvent Atoms161
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing