9XOH | pdb_00009xoh

Crystal Structure of Redesigned HasAsm Variant (14-mutation) with Iron Tetraphenylporphyrin

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, SITTING DROP	6.5	293	0.1M sodium cacodylate-HCl, 1M sodium citrate tribasic

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.274	α = 90
b = 65.357	β = 107.793
c = 74.779	γ = 90

Symmetry
Space Group	P 1 21 1

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 PILATUS3 X 6M		2025-10-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.000	SPring-8	BL45XU

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	1.51	47.1	99	0.24	0.26	0.098	0.994	6.7	6.9		101480			9.56

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	1.51	1.54	98.7		2.013	2.171	0.808	0.636	1.3	7.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.51	47.1	101456	4988	98.859	0.203	0.2014	0.1961	0.234	0.229	13.434

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]
-0.73		-0.57	2.714		-1.342

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.051
r_dihedral_angle_6_deg	14.988
r_dihedral_angle_3_deg	11.281
r_dihedral_angle_1_deg	6.65
r_lrange_it	4.474
r_lrange_other	4.375
r_scangle_it	3.226
r_scangle_other	3.225
r_scbond_it	2.126
r_scbond_other	2.126
r_mcangle_it	1.871
r_mcangle_other	1.871
r_angle_refined_deg	1.599
r_mcbond_it	1.214
r_mcbond_other	1.211
r_angle_other_deg	0.565
r_symmetry_nbd_refined	0.247
r_nbd_refined	0.225
r_symmetry_nbd_other	0.206
r_nbd_other	0.198
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.178
r_symmetry_xyhbond_nbd_other	0.152
r_symmetry_xyhbond_nbd_refined	0.15
r_symmetry_metal_ion_refined	0.121
r_metal_ion_refined	0.108
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.083
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5090
Nucleic Acid Atoms
Solvent Atoms	596
Heterogen Atoms	251

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing