9ZKF | pdb_00009zkf

Heme-containing Fungal Catalase

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		293	PEG 2000 MME

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.522	α = 90
b = 112.096	β = 90
c = 172.583	γ = 90

Symmetry
Space Group	I 2 2 2

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 EIGER2 XE 16M	Kirkpatrick-Baez (KB)	2024-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	0.97946	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.82	46.92	99.3	0.099	0.998	9.3	6.5		67659			25.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.82	1.92	96.1		0.888	0.883	0.8

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.821	30.009	65186	3213	95.346	0.205	0.2021	0.2026	0.2503	0.2501	Random selection	31.671

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]
1.631			1.144		-2.775

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.933
r_dihedral_angle_3_deg	13.472
r_dihedral_angle_2_deg	12.369
r_dihedral_angle_1_deg	7.175
r_lrange_it	6.945
r_scangle_it	5.231
r_scbond_it	3.727
r_mcangle_it	3.598
r_mcbond_it	2.611
r_angle_refined_deg	1.624
r_nbtor_refined	0.315
r_nbd_refined	0.227
r_symmetry_nbd_refined	0.17
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_refined	0.148
r_chiral_restr	0.107
r_metal_ion_refined	0.042
r_gen_planes_refined	0.009
r_bond_refined_d	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5467
Nucleic Acid Atoms
Solvent Atoms	517
Heterogen Atoms	120

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
SCALA	data scaling
PHASER	phasing