9JN4 | pdb_00009jn4

Crystal structure of KtzT-C197A in complex with HEME


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
2.7555.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.817α = 90
b = 101.256β = 90
c = 111.066γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 9M2023-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 05A1.0NSRRCTPS 05A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.812598.50.0730.0830.0390.9989.54.291871
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.8795.70.4190.4950.2580.933.4

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.8124.6987035458897.470.215480.213460.2210.252720.2595RANDOM22.423
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]
1.48-2.050.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.721
r_dihedral_angle_4_deg17.903
r_dihedral_angle_3_deg13.514
r_dihedral_angle_1_deg6.498
r_long_range_B_refined6.253
r_long_range_B_other6.024
r_scangle_other4.158
r_mcangle_it3.128
r_mcangle_other3.128
r_scbond_it2.711
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.721
r_dihedral_angle_4_deg17.903
r_dihedral_angle_3_deg13.514
r_dihedral_angle_1_deg6.498
r_long_range_B_refined6.253
r_long_range_B_other6.024
r_scangle_other4.158
r_mcangle_it3.128
r_mcangle_other3.128
r_scbond_it2.711
r_scbond_other2.711
r_mcbond_it2.141
r_mcbond_other2.141
r_angle_refined_deg1.787
r_angle_other_deg1.427
r_chiral_restr0.082
r_bond_refined_d0.012
r_gen_planes_refined0.01
r_gen_planes_other0.006
r_bond_other_d0.001
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 Atoms6432
Nucleic Acid Atoms
Solvent Atoms1006
Heterogen Atoms172

Software

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