2GED | pdb_00002ged

Signal Recognition Particle Receptor Beta-Subunit in nucleotide-free dimerized form

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH UNDER PARAFFIN OIL	5.5	277	1.3M ammonium sulfate, 50mM Bis/Tris/HCl, 0.5mM GDP, 5mM magnesium chloride, 5mM Hepes, 125mM sodium chloride, 2.5mM DTT, 0.25mM EDTA, pH 5.5, MICROBATCH UNDER PARAFFIN OIL, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.996	α = 90
b = 74.996	β = 90
c = 158.475	γ = 120

Symmetry
Space Group	P 61

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	MAR CCD 165 mm		2003-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9A	1.00944	NSLS	X9A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	33.8	98.6	0.074	24.2	5.6	33853	33373	1		49.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1NRJ chain B	2.2	25	2	25288	22942	2527	99.75	0.223	0.18832	0.18264	0.19	0.23941	0.24	RANDOM	38.144

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]
1.76	0.88		1.76		-2.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.851
r_dihedral_angle_4_deg	23.28
r_dihedral_angle_3_deg	18.004
r_dihedral_angle_1_deg	6.729
r_scangle_it	4.815
r_scbond_it	3.301
r_mcangle_it	2.331
r_angle_refined_deg	1.894
r_mcbond_it	1.641
r_angle_other_deg	1.086
r_mcbond_other	0.299
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.214
r_nbd_other	0.198
r_nbtor_refined	0.181
r_symmetry_vdw_other	0.18
r_symmetry_vdw_refined	0.147
r_chiral_restr	0.125
r_symmetry_hbond_refined	0.12
r_nbtor_other	0.092
r_bond_refined_d	0.024
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2591
Nucleic Acid Atoms
Solvent Atoms	294
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
BEAST	phasing