3T6D | pdb_00003t6d

Crystal Structure of the Reaction Centre from Blastochloris viridis strain DSM 133 (ATCC 19567) substrain-08

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DXR	Unpublished own 2.3 A model for which the 1DXR model was used in the MR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	292	Protein in 20 mM sodium phosphate buffer, 0.1% lauryldimethylamine N,N-oxide (LDAO) detergent, precipitant 1.5 M ammonium sulfate, amphiphile 3% heptanetriol, reservoir solution 2.2-2.4 M ammonium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 220.44	α = 90
b = 220.44	β = 90
c = 113.1	γ = 90

Symmetry
Space Group	P 43 21 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	MARMOSAIC 225 mm CCD	Mirrors	2007-05-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97108	ESRF	BM14

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	1.95	48.34	96.2	0.086	7.1	4.6	193320	193320			33.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2.02	98.6		0.592	1.9	4.8

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X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Unpublished own 2.3 A model for which the 1DXR model was used in the MR	1.95	48.34	193178	183501	9677	96.17	0.18343	0.18343	0.18172	0.1925	0.2163	0.2239	RANDOM	43.726

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]
0.69			0.69		-1.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.403
r_dihedral_angle_4_deg	19.191
r_dihedral_angle_3_deg	14.413
r_dihedral_angle_1_deg	5.991
r_angle_refined_deg	2.236
r_angle_other_deg	1
r_chiral_restr	0.107
r_bond_refined_d	0.019
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9339
Nucleic Acid Atoms
Solvent Atoms	861
Heterogen Atoms	1836

Software

Software
Software Name	Purpose
DNA	data collection
AMoRE	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling