3KH4 | pdb_00003kh4

Crystal structure of human Cu/Zn superoxide dismutase recombinantly produced in Leishmania tarantolae; P6522 crystal form containing 6 chains in the asymmetric unit

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	21-25% (w/v) PEG4000, 0.1 M NaOAc, pH 4.2-5.2, vapor diffusion, hanging drop, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
4.1	69.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.188	α = 90
b = 112.188	β = 90
c = 428.268	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD	SI(111)	2009-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.0	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	3.5	49.69	99.9	0.172	13.13			21168		-3	47.084

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.5	3.6	100		0.586	4.2

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		THROUGHOUT	3.5	49.69	21168	1088	99.92	0.201	0.201	0.186	0.208	0.1996	RANDOM	90.385

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]
-8.44	-4.22		-8.44		12.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.163
r_dihedral_angle_3_deg	18.979
r_dihedral_angle_4_deg	11.035
r_dihedral_angle_1_deg	7.179
r_angle_other_deg	4.332
r_scangle_it	2.63
r_angle_refined_deg	1.434
r_scbond_it	1.405
r_mcangle_it	0.933
r_mcbond_it	0.447

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.163
r_dihedral_angle_3_deg	18.979
r_dihedral_angle_4_deg	11.035
r_dihedral_angle_1_deg	7.179
r_angle_other_deg	4.332
r_scangle_it	2.63
r_angle_refined_deg	1.434
r_scbond_it	1.405
r_mcangle_it	0.933
r_mcbond_it	0.447
r_chiral_restr	0.08
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d
r_mcbond_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6660
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	12

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.