9XOK | pdb_00009xok

Crystal Structure of Redesigned HasAsm Variant (51-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, 2M ammonium sulfate, 0.2M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.282	α = 90
b = 142.558	β = 90
c = 81.231	γ = 90

Symmetry
Space Group	C 2 2 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 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	1.8	40.6	99.7	0.092	0.096	0.035	1	16.2	13.6		16787			33.27

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	1.8	1.84	99.3		2.496	2.598	0.715	0.694	1	12.8

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	1.8	40.6	16773	807	99.549	0.26	0.2564	0.2583	0.3301	0.3332	40.922

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]
0.238			-3.274		3.036

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.235
r_dihedral_angle_3_deg	14.872
r_dihedral_angle_6_deg	13.198
r_dihedral_angle_1_deg	7.793
r_lrange_other	7.61
r_lrange_it	7.604
r_scangle_it	5.371
r_scangle_other	5.368
r_mcangle_it	5.128
r_mcangle_other	5.125
r_mcbond_it	3.622
r_mcbond_other	3.617
r_scbond_it	3.529
r_scbond_other	3.527
r_angle_refined_deg	1.614
r_angle_other_deg	0.533
r_nbd_refined	0.24
r_xyhbond_nbd_refined	0.211
r_symmetry_nbd_other	0.206
r_symmetry_nbd_refined	0.194
r_nbtor_refined	0.193
r_nbd_other	0.171
r_symmetry_xyhbond_nbd_refined	0.122
r_symmetry_nbtor_other	0.096
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.055
r_bond_refined_d	0.008
r_gen_planes_refined	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	1226
Nucleic Acid Atoms
Solvent Atoms	62
Heterogen Atoms	66

Software

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