2F8T | pdb_00002f8t

Crystal structure of Aa-Ago with externally-bound siRNA

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YVU	Aa-Ago, pdb entry 1YVU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	20% PEF3350, 25mM NH4F, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.2	α = 90
b = 118.077	β = 99.57
c = 98.498	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2005-06-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	3.1	40	100	0.085		4.3		37080	1	1

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	3.11	3.23	100		0.39		4.3	3686

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	Aa-Ago, pdb entry 1YVU	3.1	40	2	31675	31675	1672	99.86	0.25	0.20868	0.20397	0.201	0.29688	0.2907	RANDOM	56.099

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]
0.47		-1.68	-0.19		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.369
r_dihedral_angle_3_deg	24.007
r_dihedral_angle_4_deg	17.905
r_dihedral_angle_1_deg	7.907
r_scangle_it	2.445
r_angle_refined_deg	1.722
r_scbond_it	1.456
r_mcangle_it	1.327
r_mcbond_it	0.725
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.276
r_nbd_refined	0.26
r_symmetry_hbond_refined	0.217
r_xyhbond_nbd_refined	0.187
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11728
Nucleic Acid Atoms	1062
Solvent Atoms	51
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MLPHARE	phasing