8QUV | pdb_00008quv

Crystal structure of chlorite dismutase at 3000 eV with no absorption corrections

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5MAU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	150 mM MgSO4, 100 mM MES pH 6.5, 20 % w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.557	α = 107.21
b = 52.755	β = 99.03
c = 54.952	γ = 109.31

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	80	PIXEL	DECTRIS PILATUS 12M		2023-05-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	4.132	Diamond	I23

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	50.35	99.43	0.997	16.51	38.8		13696

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.797			0.986

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	2.7	50.35	13042	688	99.16	0.19307	0.19091	0.1966	0.23348	0.2365	RANDOM	28.627

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]
5.41	-0.42	0.01	-1.29	-0.8	-1.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	14.83
r_dihedral_angle_1_deg	6.671
r_long_range_B_other	6.228
r_long_range_B_refined	6.226
r_scangle_other	4.637
r_dihedral_angle_2_deg	4.308
r_mcangle_other	3.383
r_mcangle_it	3.382
r_scbond_it	2.857
r_scbond_other	2.856
r_mcbond_it	2.102
r_mcbond_other	2.101
r_angle_refined_deg	1.456
r_angle_other_deg	0.491
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.007
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	3034
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	61

Software

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