1MFQ | pdb_00001mfq

Crystal Structure Analysis of a Ternary S-Domain Complex of Human Signal Recognition Particle

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L9A	PDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain)
experimental model	PDB	1JID	PDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain)
experimental model	PDB	1QB2	PDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	300.5	14% (w/v) PEG8000, 100mM Na-cacodylate, 400mM lithium sulfate, 80mM magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300.5K

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.18	α = 90
b = 131.18	β = 90
c = 204.051	γ = 120

Symmetry
Space Group	P 65 2 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		2002-02-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9393	ESRF	ID14-4

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	3.1	50	99.7	0.117	24.3	16.6		19354		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	3.1	3.21	100		0.602	6.2	15.9	1886

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS	THROUGHOUT	PDB entries 1L9A (RNA), 1JID (SRP19), 1QB2 (SRP54 M-domain)	3.1	49.63	19309	992	99.4	0.229	0.22	0.267	0.22	RANDOM	97.6

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]
-12.72	4.68		-12.72		25.45

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	16.5
c_scangle_it	8.28
c_mcangle_it	6.52
c_scbond_it	4.68
c_mcbond_it	3.68
c_improper_angle_d	1.26
c_angle_deg	1.1
c_bond_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1726
Nucleic Acid Atoms	2751
Solvent Atoms	19
Heterogen Atoms	7

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

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.