3L9E

Crystal structures of holo and Cu-deficient Cu/ZnSOD from the silkworm Bombyx mori and the implications in Amyotrophic lateral sclerosis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	289	0.2M calcium acetate, 0.1M sodium cacodylate pH 6.5, 17% PEG 4000, 15% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 289 KK

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.47	α = 90
b = 118.47	β = 90
c = 81.79	γ = 120

Symmetry
Space Group	P 65

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2007-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54178

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	2.04	23.99	97.8	0.103	11	3.9		41012

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)
	2.04	2.15	87		0.47	2.8	3.5	5335

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1AZV	2.05	23	38935	2070	99.4	0.20347	0.20113	0.24788	RANDOM	20.679

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]
0.12	0.06		0.12		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.043
r_dihedral_angle_3_deg	13.968
r_dihedral_angle_4_deg	12.623
r_dihedral_angle_1_deg	5.887
r_scangle_it	1.813
r_angle_refined_deg	1.072
r_scbond_it	1.051
r_mcangle_it	0.802
r_mcbond_it	0.6
r_nbtor_refined	0.293
r_symmetry_vdw_refined	0.2
r_nbd_refined	0.183
r_symmetry_hbond_refined	0.156
r_xyhbond_nbd_refined	0.119
r_chiral_restr	0.07
r_metal_ion_refined	0.059
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4448
Nucleic Acid Atoms
Solvent Atoms	483
Heterogen Atoms	4

Software

Software
Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling