1Z9N

X-Ray structure of a Cu-Zn superoxide dismutase from Haemophilus ducreyi with haem bound at the dimer interface

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.1	293	PEG 8000, sodium cacodylate, sodium acetate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
1.98	37.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.32	α = 66.59
b = 65.9	β = 89.87
c = 69.54	γ = 76.03

Symmetry
Space Group	P 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	CCD	MARRESEARCH	mirrors	2001-02-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9340	ESRF	ID14-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.5	19.5	93.8	0.064	0.064	10.83	3.1	88269	88269			20.284

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.59	88.6		0.278	0.278	4.53	2.99	13302

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2APS	1.5	19.5	85257	85257	4488	100	0.15834	0.15834	0.15651	0.19332	RANDOM	14.838

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]
-0.04	-0.38	-0.16	0.23	-0.28	0.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.865
r_dihedral_angle_4_deg	32.247
r_dihedral_angle_3_deg	11.735
r_dihedral_angle_1_deg	6.247
r_scangle_it	4.33
r_scbond_it	3.393
r_mcangle_it	2.168
r_mcbond_it	1.816
r_angle_refined_deg	1.514
r_angle_other_deg	0.801
r_symmetry_hbond_refined	0.277
r_mcbond_other	0.277
r_nbd_refined	0.201
r_nbd_other	0.185
r_xyhbond_nbd_refined	0.176
r_symmetry_vdw_other	0.139
r_symmetry_vdw_refined	0.116
r_chiral_restr	0.091
r_nbtor_other	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4644
Nucleic Acid Atoms
Solvent Atoms	1082
Heterogen Atoms	94

Software

Software
Software Name	Purpose
XDS	data reduction
AMoRE	phasing
REFMAC	refinement
XDS	data scaling