6OTD

Globin sensor domain of AfGcHK in monomeric form, with imidazole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5OHF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5294C4 Morpheus condition (0.09M NPS ligand stock (NaNO3, Na2HPO4, (NH4)2SO4), 0.1M buffer system pH 6.5 (imidazole, MES) and 37.5% precipitant stock MPD_P1K_P3350 (MPD, PEG 1000 and PEG 3350)
Crystal Properties
Matthews coefficientSolvent content
2.243

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.44α = 90
b = 69.44β = 90
c = 113.364γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.841.2599.20.0730.0280.99918.313.915414-3.729
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8499.91.320.5060.70314.2

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 REPLACEMENTTHROUGHOUT5OHF1.841.251541275498.660.185880.1820.231random selection35.201
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]
-0.69-0.34-0.692.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.886
r_dihedral_angle_4_deg18.874
r_dihedral_angle_3_deg15.375
r_long_range_B_refined7.571
r_long_range_B_other7.561
r_scangle_other5.836
r_dihedral_angle_1_deg4.623
r_scbond_it3.739
r_scbond_other3.737
r_mcangle_it3.714
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.886
r_dihedral_angle_4_deg18.874
r_dihedral_angle_3_deg15.375
r_long_range_B_refined7.571
r_long_range_B_other7.561
r_scangle_other5.836
r_dihedral_angle_1_deg4.623
r_scbond_it3.739
r_scbond_other3.737
r_mcangle_it3.714
r_mcangle_other3.712
r_mcbond_it2.726
r_mcbond_other2.721
r_angle_refined_deg1.7
r_angle_other_deg1.054
r_chiral_restr0.133
r_bond_refined_d0.017
r_gen_planes_refined0.01
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 Atoms1243
Nucleic Acid Atoms
Solvent Atoms68
Heterogen Atoms61

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing