6IYI

X-ray sequence and high resolution crystal structure of Starry sturgeon methemoglobin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52920.1M Hepes sodium pH 7.5, 20%(w/v) PEG4000 and 10%(v/v) 2-Propanol
Crystal Properties
Matthew coefficientSolvent content
2.5852.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.98α = 90
b = 61.41β = 97.75
c = 102.366γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2014-10-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBSRF BEAMLINE 1W2B0.9792BSRF1W2B

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
12.252.5399.080.06315.83.816020
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)
12.22.3298.90.09611.83.8

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 REPLACEMENTTHROUGHOUT3BOM2.252.531602080099.080.140460.137580.19495RANDOM18.54
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]
0.01-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.78
r_dihedral_angle_3_deg14.369
r_dihedral_angle_4_deg11.998
r_dihedral_angle_1_deg6.049
r_long_range_B_refined5.684
r_long_range_B_other5.681
r_scangle_other3.675
r_mcangle_it2.536
r_mcangle_other2.536
r_scbond_it2.367
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.78
r_dihedral_angle_3_deg14.369
r_dihedral_angle_4_deg11.998
r_dihedral_angle_1_deg6.049
r_long_range_B_refined5.684
r_long_range_B_other5.681
r_scangle_other3.675
r_mcangle_it2.536
r_mcangle_other2.536
r_scbond_it2.367
r_scbond_other2.363
r_angle_refined_deg1.863
r_mcbond_it1.606
r_mcbond_other1.603
r_angle_other_deg1.349
r_chiral_restr0.138
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_gen_planes_other0.005
r_bond_other_d0.003
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_scangle_it
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_rigid_bond_restr
r_sphericity_free
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2205
Nucleic Acid Atoms
Solvent Atoms311
Heterogen Atoms92

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing