9JN5

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	298	0.1 M ammonium acetate, 0.1 M Tris pH 8.0, 1.0 M sodium citrate

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.688	α = 90
b = 101.088	β = 90
c = 110.977	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2023-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	1.0	NSRRC	TPS 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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	25	97.6	0.113	0.125	0.054	0.998	7.4	5.4		67091

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)	Redundancy	Number Unique Reflections (All)
1	2.01	2.08	96.1		0.577	0.655	0.303	0.895		4.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2	24.95	63521	3309	96.59	0.24315	0.24008	0.2465	0.30242	0.3084	RANDOM	30.493

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]
1.93			-2.35		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.569
r_dihedral_angle_4_deg	17.572
r_dihedral_angle_3_deg	14.586
r_long_range_B_refined	6.9
r_long_range_B_other	6.9
r_dihedral_angle_1_deg	6.776
r_scangle_other	4.524
r_mcangle_it	3.76
r_mcangle_other	3.76
r_scbond_it	2.909
r_scbond_other	2.909
r_mcbond_it	2.563
r_mcbond_other	2.562
r_angle_refined_deg	1.659
r_angle_other_deg	1.36
r_chiral_restr	0.07
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.005
r_bond_other_d	0.002
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 Atoms	Number
Protein Atoms	6427
Nucleic Acid Atoms
Solvent Atoms	744
Heterogen Atoms	192

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHASER	phasing