3X39 | pdb_00003x39

Domain-swapped dimer of Pseudomonas aeruginosa cytochrome c551

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	351C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1M HEPES-NaOH buffer containing 1.4M sodium citrate tribasic dehydrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.611	α = 90
b = 82.611	β = 90
c = 89.828	γ = 120

Symmetry
Space Group	P 63 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	ADSC QUANTUM 315		2010-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	0.8	SPring-8	BL38B1

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	50	99.9	0.062	0.062	57.942	20.7	30970	29583		-3

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	1.55	100		0.551	0.551	7.026	20.6	2893

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	351C	1.5	50	27950	1495	99.51	0.14178	0.13946	0.14	0.18814	0.19	RANDOM	28.196

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]
0.52	0.26		0.52		-1.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	44.52
r_sphericity_free	30.695
r_sphericity_bonded	15.869
r_dihedral_angle_3_deg	11.435
r_dihedral_angle_4_deg	9.369
r_dihedral_angle_1_deg	5.604
r_long_range_B_refined	5.138
r_scangle_other	4.719
r_long_range_B_other	4.618
r_scbond_it	4.161
r_scbond_other	4.15
r_mcangle_other	3.858
r_mcangle_it	3.844
r_mcbond_it	3.167
r_mcbond_other	3.092
r_rigid_bond_restr	2.696
r_angle_refined_deg	1.604
r_angle_other_deg	0.931
r_chiral_restr	0.137
r_gen_planes_other	0.014
r_gen_planes_refined	0.012
r_bond_refined_d	0.011
r_bond_other_d	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1220
Nucleic Acid Atoms
Solvent Atoms	191
Heterogen Atoms	86

Software

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