2BNP | pdb_00002bnp

Lipidic cubic phase grown reaction centre from Rhodobacter sphaeroides, ground state

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	7.5		60% MONOOLEIN/40% 25 MG/ML PROT. (4:1)18% JEFFAMINE M-600, 1M HEPES PH7.5, 0.7M AMM.SULF, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.8	55.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.142	α = 90
b = 100.142	β = 90
c = 238.002	γ = 90

Symmetry
Space Group	P 42 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	ADSC CCD	GE MIRROR	2004-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	2.7	120	99.3	0.18	11.4	6.2		32255		2

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	2.7	2.79	100		0.79	2.1	6.3

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 1OGV	2.7	39.53	32254	1696	99.4	0.212	0.21	0.23	0.249	0.26	RANDOM	31.19

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]
-0.04			-0.04		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.583
r_angle_refined_deg	2.321
r_scangle_it	1.623
r_scbond_it	1.134
r_angle_other_deg	0.849
r_mcangle_it	0.693
r_mcbond_it	0.378
r_nbd_other	0.223
r_nbd_refined	0.193
r_symmetry_vdw_other	0.151
r_xyhbond_nbd_refined	0.127
r_nbtor_other	0.085
r_chiral_restr	0.083
r_symmetry_vdw_refined	0.075
r_symmetry_hbond_refined	0.075
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
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_mcbond_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	6440
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	431

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling