2ZXY | pdb_00002zxy

Crystal Structure of Cytochrome c555 from Aquifex aeolicus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	277	39% PEG 4000, 0.8M ammonium acetate, 0.1M tri-sodium citrate dehydrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
1.94	36.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.529	α = 90
b = 32.993	β = 115.05
c = 49.668	γ = 90

Symmetry
Space Group	C 1 2 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	RIGAKU JUPITER 210		2007-11-27	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	RIGAKU JUPITER 210		2007-11-27	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	0.7	SPring-8	BL38B1
2	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.73786, 1.74011, 1.69260	SPring-8	BL38B1

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	1.15	50	97	0.047		3.71		25402

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.15	1.19	89.4		10.01

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	MAD	THROUGHOUT	1.15	15.92	23375	1257	97.56	0.12899	0.12711	0.13	0.16386	0.16	RANDOM	10.536

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.677
r_sphericity_free	14.002
r_dihedral_angle_3_deg	13.816
r_dihedral_angle_1_deg	12.278
r_sphericity_bonded	6.455
r_scangle_it	6.241
r_scbond_it	4.903
r_mcangle_it	3.579
r_rigid_bond_restr	3.165
r_mcbond_it	2.628
r_angle_refined_deg	0.93
r_nbd_refined	0.342
r_symmetry_vdw_refined	0.328
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.26
r_xyhbond_nbd_refined	0.212
r_chiral_restr	0.057
r_gen_planes_refined	0.023
r_bond_refined_d	0.01
r_metal_ion_refined	0.004
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	711
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	43

Software

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