2WP8

yeast rrp44 nuclease

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NN6	PDB ENTRIES 2NN6, 2VNU
experimental model	PDB	2VNU	PDB ENTRIES 2NN6, 2VNU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8		7.5 % (W/V) OF PEG 20.000, 50 MM TRIS PH 8.0 AND 10% (W/V) GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.86	57.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.9	α = 90
b = 125.68	β = 90
c = 139.4	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESEARCH		2009-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	20	100	0.01	21	10		39670		2

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	3.2	100		0.05	5.6

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 ENTRIES 2NN6, 2VNU	3	19.99	38325	1185	100	0.20899	0.20698	0.21	0.27291	0.27	RANDOM	24.452

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]
			0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.758
r_dihedral_angle_3_deg	18.127
r_dihedral_angle_4_deg	17.87
r_dihedral_angle_1_deg	7.388
r_scangle_it	2.364
r_angle_refined_deg	1.508
r_scbond_it	1.365
r_mcangle_it	0.938
r_angle_other_deg	0.936
r_mcbond_it	0.486
r_chiral_restr	0.082
r_mcbond_other	0.074
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10809
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing