2EB1

Crystal Structure of the C-Terminal RNase III Domain of Human Dicer

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	278	1.0M ammonium sulfate, 0.1M TRIS-HCL, 0.01M MGCL2, pH 8.00, VAPOR DIFFUSION, SITTING DROP, temperature 278K

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.602	α = 90
b = 199.743	β = 90
c = 119.64	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 4		2005-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0000	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	50					72223

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 (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 1JFZ	2	50	68021	3627	99.7	0.212	0.211	0.22	0.234	0.21	RANDOM	40.46

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]
-0.14			-2.03		2.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.361
r_scangle_it	4.971
r_angle_other_deg	3.576
r_scbond_it	3.026
r_mcangle_it	2.731
r_mcbond_it	1.796
r_angle_refined_deg	1.483
r_symmetry_vdw_other	0.291
r_nbd_other	0.278
r_nbd_refined	0.239
r_symmetry_vdw_refined	0.188
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.176
r_metal_ion_refined	0.158
r_chiral_restr	0.102
r_nbtor_other	0.102
r_bond_refined_d	0.02
r_gen_planes_other	0.01
r_gen_planes_refined	0.008
r_bond_other_d
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4206
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	6

Software

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