8S6C | pdb_00008s6c

Crystal structure of Cyanobacterium TDX16 peroxidase

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	293	PEG6000, MES buffer, Magnesium chloride or Calcium chloride

Crystal Properties
Matthews coefficient	Solvent content
1.9	34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.667	α = 90
b = 72.541	β = 95.85
c = 56.203	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 2M		2023-11-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9655	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.737	55.91	97.9	0.112	0.047	0.997	9.2	6.7		42540

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	1.74	1.78	100		0.832	0.419		5.7

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.74	55.91	40436	2072	97.8	0.15269	0.15088	0.162	0.18784	0.1908	RANDOM	26.798

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]
1.72		0.29	-0.93		-0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	11.853
r_dihedral_angle_1_deg	6.477
r_dihedral_angle_2_deg	5.778
r_long_range_B_refined	5.219
r_long_range_B_other	5.106
r_scangle_other	3.946
r_mcangle_it	2.986
r_mcangle_other	2.986
r_scbond_it	2.702
r_scbond_other	2.702
r_mcbond_it	2.071
r_mcbond_other	2.07
r_angle_refined_deg	1.627
r_angle_other_deg	0.72
r_chiral_restr	0.081
r_gen_planes_other	0.009
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3950
Nucleic Acid Atoms
Solvent Atoms	363
Heterogen Atoms	52

Software

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