9JN6 | pdb_00009jn6

Crystal structure of KtzT-C197A in complex with HEME and product


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72980.1 M ammonium acetate, 0.1 M Tris pH 8.0, 1.0 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.7355.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.878α = 90
b = 101.613β = 90
c = 111.155γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2023-12-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A0.99987NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7229.2497.60.99913.957.5109356
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.8296.60.952.595.2

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7229.24107504199999.210.187660.187020.1960.221960.2294RANDOM24.659
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]
0.97-1.680.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.382
r_dihedral_angle_4_deg16.563
r_dihedral_angle_3_deg13.765
r_long_range_B_refined6.89
r_long_range_B_other6.89
r_dihedral_angle_1_deg6.466
r_scangle_other5.097
r_mcangle_other3.5
r_mcangle_it3.499
r_scbond_it3.348
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.382
r_dihedral_angle_4_deg16.563
r_dihedral_angle_3_deg13.765
r_long_range_B_refined6.89
r_long_range_B_other6.89
r_dihedral_angle_1_deg6.466
r_scangle_other5.097
r_mcangle_other3.5
r_mcangle_it3.499
r_scbond_it3.348
r_scbond_other3.348
r_mcbond_it2.339
r_mcbond_other2.339
r_angle_refined_deg1.823
r_angle_other_deg1.561
r_chiral_restr0.086
r_bond_refined_d0.013
r_gen_planes_refined0.011
r_gen_planes_other0.006
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 Atoms6443
Nucleic Acid Atoms
Solvent Atoms851
Heterogen Atoms199

Software

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