3D38 | pdb_00003d38

Crystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2I5N	PDB entry 2I5N

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Plug-based Microfluidics	6	296	9 mg/mL Protein, 4.6 mM LDAO, 10 mM Methyl-beta-cyclodextrin, 1.6-1.7 M Sulfate, 4.5% w/v Triethylammonium phosphate pH 6.0, 3% 1,2,3-heptanetriol, 30 mM NaH2PO4-Na2HPO4 pH 6.0, Plug-based Microfluidics, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
7.19	82.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 241.171	α = 90
b = 241.171	β = 90
c = 113.391	γ = 120

Symmetry
Space Group	P 31 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	MARMOSAIC 300 mm CCD		2008-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

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	3.2	50	99.8	0.168	30.3	6	62037	62037

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	PDB entry 2I5N	3.21	50	62025	3145	99.58	0.194	0.192	0.1958	0.224	0.2277	RANDOM	67.435

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]
3.88	1.94		3.88		-5.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.642
r_dihedral_angle_3_deg	17.749
r_dihedral_angle_4_deg	15.265
r_dihedral_angle_1_deg	5.634
r_scangle_it	2.275
r_angle_refined_deg	1.437
r_scbond_it	1.302
r_mcangle_it	1.073
r_mcbond_it	0.552
r_chiral_restr	0.085

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.642
r_dihedral_angle_3_deg	17.749
r_dihedral_angle_4_deg	15.265
r_dihedral_angle_1_deg	5.634
r_scangle_it	2.275
r_angle_refined_deg	1.437
r_scbond_it	1.302
r_mcangle_it	1.073
r_mcbond_it	0.552
r_chiral_restr	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9282
Nucleic Acid Atoms
Solvent Atoms	159
Heterogen Atoms	870

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.