8AVK | pdb_00008avk

Superoxide dismutase SodFM1 from CPR Parkubacteria Wolfebacteria

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IX9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	100 mM sodium acetate trihydrate pH 4.5 and 25% w/v polyethylene glycol 3350.

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.531	α = 90
b = 70.586	β = 100.301
c = 57.788	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 EIGER2 X 16M		2021-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.89843	Diamond	I03

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	2.1	70.59	100	0.996	7.3	14.1		21632

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	2.1	2.16			0.64	1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	FREE R-VALUE	1IX9	2.1	56.857	21594	1048	99.907	0.211	0.2089	0.21	0.2563	0.26	37.345

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]
-1.993		1.639	2.519		-1.052

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.401
r_dihedral_angle_6_deg	15.353
r_dihedral_angle_1_deg	6.541
r_lrange_other	5.666
r_lrange_it	5.664
r_scangle_it	4.805
r_scangle_other	4.804
r_dihedral_angle_2_deg	4.656
r_mcangle_it	3.595
r_mcangle_other	3.595
r_scbond_it	3.41
r_scbond_other	3.409
r_mcbond_it	2.631
r_mcbond_other	2.62
r_angle_refined_deg	1.827
r_angle_other_deg	0.625
r_nbd_other	0.247
r_nbd_refined	0.243
r_symmetry_nbd_refined	0.234
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.196
r_xyhbond_nbd_refined	0.142
r_ncsr_local_group_1	0.098
r_chiral_restr	0.09
r_symmetry_nbtor_other	0.084
r_symmetry_xyhbond_nbd_refined	0.076
r_symmetry_xyhbond_nbd_other	0.039
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_metal_ion_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3308
Nucleic Acid Atoms
Solvent Atoms	11
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing
BUCCANEER	model building
Coot	model building