3CE1 | pdb_00003ce1

Crystal Structure of the Cu/Zn Superoxide Dismutase from Cryptococcus liquefaciens Strain N6

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1F1G	PDB ENTRY 1F1G

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	30% PEG 4000, 0.2M sodium acetate, 0.1M Tris-Cl , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.854	α = 90
b = 111.768	β = 90
c = 70.456	γ = 90

Symmetry
Space Group	C 2 2 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	CCD	ADSC QUANTUM 315	KB MIRRORS	2004-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.000	SPring-8	BL41XU

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	1.2	70.53	99.9	0.065	31.3	7	44741	44741

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)
	1.2	1.24	99.5		0.459	3.5	6.3	4372

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	PDB ENTRY 1F1G	1.2	50	44698	44698	2249	99.87	0.15	0.15	0.149	0.15	0.166	0.17	RANDOM	10.769

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]
			-0.25		0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.231
r_dihedral_angle_4_deg	12.736
r_dihedral_angle_3_deg	9.205
r_sphericity_free	7.475
r_dihedral_angle_1_deg	6.395
r_sphericity_bonded	4.028
r_scangle_it	3.216
r_scbond_it	2.55
r_mcangle_it	2.163
r_rigid_bond_restr	1.706
r_mcbond_it	1.496
r_angle_refined_deg	1.362
r_nbtor_refined	0.309
r_symmetry_hbond_refined	0.249
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.177
r_symmetry_vdw_refined	0.161
r_chiral_restr	0.089
r_metal_ion_refined	0.044
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1078
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms	6

Software

Software
Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling