1NKZ | pdb_00001nkz

Crystal structure of LH2 B800-850 from Rps. acidophila at 2.0 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	9.3	289	1.0 M Phosphate, 2.5% Benzamidine, 0.75 % Beta-octylglucoside, 25-250 mM NaCl equilibrated against 2.3 M Ammonium Sulphate at pH 9.5, pH 9.3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
4.05	69.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.052	α = 90
b = 117.052	β = 90
c = 298.438	γ = 120

Symmetry
Space Group	H 3 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	VERTICALLY FOCUSING 1.2M Si MIRROR, MONOCHROMATED WITH A HORIZONTALLY FOCUSED Si(111) CRYSTAL	1997-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX9.6	0.87	SRS	PX9.6

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	33		0.051	8.7	4.1	49320	48976

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	2.05	95		0.306	2.5	3.3

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 1KZU	2	8	52374	48976	2431	99.3	0.1704	0.16943	0.18	0.19006	RANDOM	22.962

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]
1.03	0.51		1.03		-1.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.484
r_scangle_it	2.61
r_scbond_it	1.941
r_angle_refined_deg	1.621
r_angle_other_deg	1.508
r_mcangle_it	1.487
r_mcbond_it	0.845
r_chiral_restr	0.512
r_symmetry_hbond_refined	0.408
r_symmetry_vdw_other	0.369
r_symmetry_vdw_refined	0.358
r_xyhbond_nbd_refined	0.342
r_nbd_refined	0.274
r_nbd_other	0.269
r_nbtor_other	0.107
r_gen_planes_other	0.04
r_bond_refined_d	0.019
r_gen_planes_refined	0.019
r_bond_other_d	0.014
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2178
Nucleic Acid Atoms
Solvent Atoms	230
Heterogen Atoms	1053

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
DM	model building
REFMAC	refinement
CCP4	data scaling
DM	phasing