9XPI | pdb_00009xpi

Crystal Structure of Redesigned HasAsm Variant (48-mutation) with Heme

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	8	293	0.1M imidazole-HCl, 2.5M NaCl, 0.2M Zinc acetate

Crystal Properties
Matthews coefficient	Solvent content
3.25	62.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.183	α = 90
b = 69.183	β = 90
c = 86.555	γ = 120

Symmetry
Space Group	P 31 2 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		2025-11-04	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	2.16	43.28	99.9	0.111	0.114	0.026	0.999	21	19.7		13312			49.13

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	2.16	2.23	99.9		1.475	1.511	0.327	0.987	3.7	21.1

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	2.161	35.1	13286	682	99.932	0.222	0.2203	0.2208	0.2547	0.2554	51.431

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]
1.842	0.921		1.842		-5.977

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.719
r_dihedral_angle_6_deg	14.421
r_lrange_other	10.071
r_lrange_it	10.064
r_scangle_it	8.625
r_scangle_other	8.624
r_dihedral_angle_2_deg	7.611
r_dihedral_angle_1_deg	7.08
r_scbond_it	6.566
r_scbond_other	6.086
r_mcangle_it	5.593
r_mcangle_other	5.591
r_mcbond_it	4.127
r_mcbond_other	4.107
r_angle_refined_deg	2.03
r_angle_other_deg	0.542
r_symmetry_xyhbond_nbd_refined	0.344
r_nbd_other	0.293
r_symmetry_nbd_refined	0.278
r_xyhbond_nbd_refined	0.251
r_nbd_refined	0.233
r_symmetry_nbd_other	0.216
r_nbtor_refined	0.19
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.07
r_bond_refined_d	0.018
r_gen_planes_other	0.012
r_gen_planes_refined	0.009
r_bond_other_d
r_dihedral_angle_other_2_deg

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1295
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	61

Software

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