6QV9

Staphylococcus aureus superoxide dismutase SodA double mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6EX3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	200 mM MgCl2, 100 mM Bis-Tris pH 5.5, 25% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.2	43.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.25	α = 90
b = 68.15	β = 100.58
c = 57.29	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 PILATUS 6M		2018-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	1.550	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	1.8	43.46	99.4	0.995	10.9	6		36588

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	1.8	1.84	96.4		0.73	2.2	4

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 (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	6EX3	1.8	35.77	34541	1735	98.87	0.17252	0.17076	0.18	0.20685	0.21	RANDOM	21.466

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]
0.47		-1.65	-0.73		0.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.038
r_dihedral_angle_3_deg	12.706
r_dihedral_angle_4_deg	6.422
r_dihedral_angle_1_deg	6.259
r_long_range_B_refined	5.963
r_long_range_B_other	5.961
r_scangle_other	5.232
r_scbond_it	3.249
r_scbond_other	3.248
r_mcangle_it	2.843
r_mcangle_other	2.842
r_mcbond_it	1.92
r_mcbond_other	1.915
r_angle_refined_deg	1.559
r_angle_other_deg	1.475
r_chiral_restr	0.086
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
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	3198
Nucleic Acid Atoms
Solvent Atoms	133
Heterogen Atoms	2

Software

Software
Software Name	Purpose
GDA	data collection
xia2	data reduction
XDS	data scaling
Aimless	data scaling
MOLREP	phasing
Coot	model building
REFMAC	refinement