2I5N | pdb_00002i5n

1.96 A X-ray structure of photosynthetic reaction center from Rhodopseudomonas viridis:Crystals grown by microfluidic technique

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DXR	PDB ENTRY 1DXR

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				THE CRYSTALS WERE GROWN BY MICROFLUIDIC TECHNIQUE USING CRYSTALLIZATION BUFFER: 1.6 - 1.8 M (NH4)2SO4 IN TRIS PH 7.8. THE ADDITIVES WERE HEPTANETRIOL (3%, W/V) AND 2% TRIETHYL AMONIUM PHOSPHATE. THE DETERGENT WAS LAURYL DIMETHYLAMINE-N-OXIDE (LDA). THE PROTEIN COMPLEX WAS IN SODIUM PHOSPHATE BUFFER PH 6.0 AND 0.08% LDA.

Crystal Properties
Matthews coefficient	Solvent content
5	70

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 220.4	α = 90
b = 220.4	β = 90
c = 113.009	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		CCD	MARMOSAIC 300 mm CCD	ADJUSTABLE FOCUSING MIRRORS	2006-07-17	M	SINGLE WAVELENGTH

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

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	1.96	20	94.5	0.082	17.5	5.9		189189			24.5

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	1.96	2	67.4		0.48	2.3	4.1

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 (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 1DXR	1.96	20	189189	189189	9533	96.5	0.173	0.172	0.1783	0.19	0.1953	RANDOM	25.42

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]
0.35			0.35		-0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.902
r_dihedral_angle_4_deg	16.534
r_dihedral_angle_3_deg	12.261
r_dihedral_angle_1_deg	5.683
r_scangle_it	3.506
r_scbond_it	2.507
r_mcangle_it	1.659
r_angle_refined_deg	1.329
r_mcbond_it	1.117
r_angle_other_deg	1.055
r_mcbond_other	0.32
r_symmetry_vdw_refined	0.235
r_nbd_refined	0.224
r_symmetry_vdw_other	0.222
r_nbtor_refined	0.203
r_nbd_other	0.195
r_symmetry_hbond_refined	0.124
r_xyhbond_nbd_refined	0.114
r_nbtor_other	0.085
r_chiral_restr	0.065
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9282
Nucleic Acid Atoms
Solvent Atoms	771
Heterogen Atoms	970

Software

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