2GNU | pdb_00002gnu

The crystallization of reaction center from Rhodobacter sphaeroides occurs via a new route

X-RAY DIFFRACTION

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	VAPOR DIFFUSION, HANGING DROP	8.1	293	20% jeffamine M600, 1M HEPES, 0.7M (NH4)2SO4, 2.5% 1,2,3-heptanetriol, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.28	62.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.422	α = 90
b = 100.422	β = 90
c = 235.412	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 QUANTUM 4		2005-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	117.851	99.8	0.117	0.117	5.6	10.2		61848

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32		100	0.641	0.641	0.9	4.9

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 (All)	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	2.2	19.8	61641	3129	99.57	0.202	0.2	0.2	0.246	0.25	RANDOM	26.641

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]
0.03			0.03		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.404
r_dihedral_angle_4_deg	21.447
r_dihedral_angle_3_deg	17.782
r_dihedral_angle_1_deg	6.176
r_scangle_it	3.249
r_angle_refined_deg	2.658
r_scbond_it	2.091
r_mcangle_it	1.627
r_mcbond_it	1.004
r_nbtor_refined	0.317

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.404
r_dihedral_angle_4_deg	21.447
r_dihedral_angle_3_deg	17.782
r_dihedral_angle_1_deg	6.176
r_scangle_it	3.249
r_angle_refined_deg	2.658
r_scbond_it	2.091
r_mcangle_it	1.627
r_mcbond_it	1.004
r_nbtor_refined	0.317
r_nbd_refined	0.227
r_symmetry_vdw_refined	0.212
r_chiral_restr	0.166
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_refined	0.145
r_bond_refined_d	0.02
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6419
Nucleic Acid Atoms
Solvent Atoms	155
Heterogen Atoms	471

Software

Software
Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

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.