3KTV | pdb_00003ktv

Crystal structure of the human SRP19/S-domain SRP RNA complex

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LNG	PDB entry 1LNG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	291	100 mM NaOAc, 0.75 M KF, 2.2 M (NH4)2SO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.68	66.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.12	α = 90
b = 100.12	β = 90
c = 293.3	γ = 90

Symmetry
Space Group	P 43 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	MARMOSAIC 225 mm CCD	mirrors	2009-04-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.87260	ESRF	ID23-2

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	3.8	70.2	96.1	0.103	7.3		15622	14852

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)
1	3.8	4.01	97.9		0.608	1.3	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 (All)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1LNG	3.8	70.01	14727	711	94.28	0.293	0.293	0.291	0.329	0.2941	RANDOM	88.009

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.193
r_dihedral_angle_3_deg	17.281
r_dihedral_angle_4_deg	12.058
r_dihedral_angle_1_deg	5.666
SIDE-CHAIN ANGLE REFINED ATOMS (A''2)	1.576
r_angle_refined_deg	1.352
MAIN-CHAIN ANGLE REFINED ATOMS (A''2)	0.924
SIDE-CHAIN BOND REFINED ATOMS (A''2)	0.894
MAIN-CHAIN BOND REFINED ATOMS (A''2)	0.494
CHIRAL-CENTER RESTRAINTS (A''3)	0.058
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1725
Nucleic Acid Atoms	4659
Solvent Atoms
Heterogen Atoms	6

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing