2WJN

Lipidic sponge phase crystal structure of photosynthetic reaction centre from Blastochloris viridis (high dose)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PRC	PDB ENTRY 2PRC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	8		MONOOLEIN WAS MIXED WITH WATER IN RATIO OF 60:40 (W/W) UNTIL A VISCOUS NON-BIREFRINGENT LCP WAS FORMED. THEREAFTER, LIPIDIC-SPONGE PHASE INITIATING SOLUTION (20% JEFFAMINE M600, 1M HEPES PH=8.0, 0.7M (NH4)2SO4 AND 2.5% 1,2,3-HEPTANETRIOL) WAS ADDED IN A RATIO OF 1 TO 4 (V/V) AND EQUILIBRATED UNTIL PHASE SEPARATION HAS OCCURRED. THE UPPER LIPIDIC-SPONGE PHASE WAS HARVESTED AND 1UL WAS USED AS A PRECIPITANT SOLUTION TOGETHER WITH 1UL OF 25 MG/ML PROTEIN SOLUTION IN A HANGING-DROP, VAPOUR-DIFFUSION EXPERIMENT. TO IMPROVE CRYSTAL QUALITY 1UL OF ADDITIVE 1M TRI-NA-CITRATE HAS BEEN ADDED TO THE CRYSTALLIZATION DROP.

Crystal Properties
Matthews coefficient	Solvent content
2.67	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 84.76	α = 90
b = 139.43	β = 90
c = 178.24	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS 6M	MIRRORS	2008-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	1.85	44.99	97.8	0.08	14.97	6.55		176119		2	32.5

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	1.85	2	92.1		0.48	3.72	6.74

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2PRC	1.86	44.97	167284	8832	99.38	0.17185	0.17071	0.19326	RANDOM	29.528

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]
-0.61			3.38		-2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.822
r_dihedral_angle_4_deg	15.685
r_dihedral_angle_3_deg	12.389
r_dihedral_angle_1_deg	5.834
r_scangle_it	3.126
r_angle_refined_deg	2.253
r_scbond_it	2.216
r_mcangle_it	1.444
r_angle_other_deg	1.169
r_mcbond_it	0.962
r_mcbond_other	0.287
r_nbd_refined	0.244
r_nbd_other	0.205
r_nbtor_refined	0.188
r_symmetry_vdw_other	0.164
r_xyhbond_nbd_refined	0.157
r_symmetry_vdw_refined	0.144
r_chiral_restr	0.136
r_symmetry_hbond_refined	0.127
r_nbtor_other	0.088
r_metal_ion_refined	0.063
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9185
Nucleic Acid Atoms
Solvent Atoms	692
Heterogen Atoms	713

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing