7B4P | pdb_00007b4p

A Bacteroidetes bacterium CuZn-superoxide dismutase with CuZn metalation

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7B4O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	.12 M alcohol mix containing 1,6-hexanediol, 1-butanol 1,2-propanediol, 2-propanol, 4-butanediol, 1,3-propanediol; 0.1 M buffer mix containing sodium 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid, 3-(N-morpholino)propane sulfonic acid pH 7.5; 37.5 % precipitant mix containing 2-Methyl-2,4-pentanediol, polyethylene glycol 1000, polyethylene glycol 3350

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.79	α = 90
b = 109.593	β = 90
c = 122.598	γ = 90

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2020-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.9786	SOLEIL	PROXIMA 1

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	81.71	100	0.999	10.6	9.2		16195

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	2.83			0.61

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	7B4O	2.7	81.7	16146	803	99.963	0.242	0.2396	0.25	0.2783	0.28	89.467

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]
0.931			2.595		-3.526

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.359
r_dihedral_angle_3_deg	12.751
r_dihedral_angle_4_deg	6.934
r_dihedral_angle_1_deg	5.934
r_lrange_it	3.668
r_lrange_other	3.667
r_angle_refined_deg	1.213
r_angle_other_deg	1.067
r_mcangle_it	0.81
r_mcangle_other	0.81
r_scangle_it	0.56
r_scangle_other	0.56
r_mcbond_it	0.45
r_mcbond_other	0.45
r_scbond_it	0.299
r_scbond_other	0.299
r_symmetry_nbd_refined	0.184
r_nbd_other	0.176
r_nbd_refined	0.154
r_symmetry_nbd_other	0.151
r_nbtor_refined	0.133
r_xyhbond_nbd_refined	0.088
r_symmetry_nbtor_other	0.064
r_ncsr_local_group_5	0.064
r_ncsr_local_group_6	0.064
r_ncsr_local_group_1	0.062
r_ncsr_local_group_3	0.062
r_ncsr_local_group_4	0.061
r_ncsr_local_group_2	0.045
r_metal_ion_refined	0.038
r_chiral_restr	0.031
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4427
Nucleic Acid Atoms
Solvent Atoms	21
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data reduction
Aimless	data scaling
MOLREP	phasing