5XEC | pdb_00005xec

Heterodimer constructed from PA cyt c551-HT cyt c552 and HT cyt c552-PA cyt c551 chimeric proteins

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	351C	351C, 1YNR
experimental model	PDB	1YNR	351C, 1YNR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	100 mM Tris-HCl containing 200 mM sodium acetate, 30% w/v PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.21	44.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.35	α = 90
b = 72.54	β = 106.07
c = 35.01	γ = 90

Symmetry
Space Group	P 1 21 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	RAYONIX MX225HE		2015-01-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0000	SPring-8	BL38B1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	1.1	20	99.3	0.078	0.997	7.8	3.5		60431

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.16	100		0.389	0.843	2.7	3.5

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, 1YNR	1.1	20	57400	2984	99.2	0.17578	0.17467	0.18	0.19731	0.2	RANDOM	12.396

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]
0.16		0.19	-0.37		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.488
r_sphericity_free	22.252
r_dihedral_angle_3_deg	11.204
r_sphericity_bonded	8.229
r_dihedral_angle_1_deg	5.229
r_long_range_B_refined	2.789
r_dihedral_angle_4_deg	2.36
r_long_range_B_other	2.292
r_scangle_other	1.854
r_rigid_bond_restr	1.628
r_scbond_it	1.61
r_scbond_other	1.608
r_angle_refined_deg	1.408
r_mcangle_it	1.338
r_mcangle_other	1.338
r_mcbond_it	1.024
r_mcbond_other	1.023
r_angle_other_deg	0.839
r_chiral_restr	0.117
r_gen_planes_refined	0.012
r_bond_refined_d	0.01
r_gen_planes_other	0.01
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	1211
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing