9XPD | pdb_00009xpd

Crystal Structure of Redesigned HasAsm Variant (51-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, 1M sodium citrate tribasic

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.357	α = 90
b = 140.528	β = 90
c = 80.708	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	1.22	35	99.9	0.145	0.152	0.043	0.998	12.3	12.9		51927			11.11

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.22	1.24	99.4		0.876	0.659	1.6	13.3

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	1.22	35	51900	2633	99.783	0.156	0.1549	0.1547	0.1775	0.178	17.589

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]
-0.267			-0.04		0.307

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.516
r_lrange_it	12.246
r_lrange_other	12.055
r_scangle_it	10.369
r_scangle_other	10.365
r_dihedral_angle_3_deg	10.296
r_dihedral_angle_2_deg	10.131
r_scbond_other	7.427
r_scbond_it	7.391
r_mcangle_other	6.578
r_mcangle_it	6.569
r_dihedral_angle_1_deg	6.004
r_mcbond_it	4.61
r_mcbond_other	4.578
r_rigid_bond_restr	4.198
r_angle_refined_deg	1.935
r_angle_other_deg	0.687
r_dihedral_angle_other_2_deg	0.657
r_symmetry_nbd_refined	0.294
r_metal_ion_refined	0.269
r_nbd_refined	0.226
r_nbd_other	0.22
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.171
r_symmetry_xyhbond_nbd_refined	0.145
r_chiral_restr	0.107
r_symmetry_metal_ion_refined	0.104
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_other	0.03
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1282
Nucleic Acid Atoms
Solvent Atoms	92
Heterogen Atoms	69

Software

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