1L9J | pdb_00001l9j

X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1AIJ	PDB ID Code 1AIJ and 1CXC are starting models for the reaction center and cytochrome c2 respectively. RESIDUES LISTED IN REMARK 465 ARE MISSING DUE TO LACK OF ELECTRON DENSITY. ATOMS ON THE ISOPRENOID TAIL OF BCL 1001 and 2001, BPH 1005 and 2005, AND U10 1008 and 2008 ARE MISSING DUE TO THE LACK OF ELECTRON DENSITY.
experimental model	PDB	1CXC	PDB ID Code 1AIJ and 1CXC are starting models for the reaction center and cytochrome c2 respectively. RESIDUES LISTED IN REMARK 465 ARE MISSING DUE TO LACK OF ELECTRON DENSITY. ATOMS ON THE ISOPRENOID TAIL OF BCL 1001 and 2001, BPH 1005 and 2005, AND U10 1008 and 2008 ARE MISSING DUE TO THE LACK OF ELECTRON DENSITY.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	292	PEG 4000, lauryl-dimethylamine-N-oxide, heptane-1,2,3-triol, tricine buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
3.59	65.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.93	α = 90
b = 80.312	β = 92.41
c = 246.575	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	IMAGE PLATE	MARRESEARCH	Flat mirror (vertical focusing)	2000-06-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.98	SSRL	BL9-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	3.25	49.32	98.9	0.119	4.8	7.3	47751	47751			64.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.25	3.43	98.7		0.45	1.7	7.4	6920

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID Code 1AIJ and 1CXC are starting models for the reaction center and cytochrome c2 respectively. RESIDUES LISTED IN REMARK 465 ARE MISSING DUE TO LACK OF ELECTRON DENSITY. ATOMS ON THE ISOPRENOID TAIL OF BCL 1001 and 2001, BPH 1005 and 2005, AND U10 1008 and 2008 ARE MISSING DUE TO THE LACK OF ELECTRON DENSITY.	3.25	49.32	47695	47695	2385	98.5	0.263	0.263	0.248	0.2383	0.287	0.275	random	74.9

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]
46.477		-11.191	-21.432		-25.045

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	19.25
c_angle_d	1.28
c_improper_angle_d	0.883
c_bond_d	0.00773

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14404
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	964

Software

Software
Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CNS	phasing