2A1S

Crystal structure of native PARN nuclease domain

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2A1R	PDB ENTRY 2A1R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	PEG3350, 0.2M ammonium tartrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.42	48.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 205.54	α = 90
b = 123.016	β = 112.59
c = 82.844	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	ADSC QUANTUM 210		2004-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9791	ESRF	ID29

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	2.6	50	99.5	0.079	6.2	3.5	58187	58173	2	2	69.76

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	2.6	2.69	99.6		0.628	2	3.5	5683

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2A1R	2.6	20	3	3	58173	56251	1780	99.41	0.243	0.21971	0.21864	0.25362	RANDOM	52.465

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]
1		2.19	2.09		-1.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.132
r_scangle_it	2.613
r_mcangle_it	1.51
r_scbond_it	1.48
r_angle_refined_deg	1.334
r_angle_other_deg	0.815
r_mcbond_it	0.796
r_symmetry_vdw_other	0.247
r_nbd_other	0.228
r_symmetry_hbond_refined	0.225
r_nbd_refined	0.212
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.188
r_nbtor_other	0.088
r_chiral_restr	0.078
r_bond_refined_d	0.013
r_gen_planes_refined	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12876
Nucleic Acid Atoms
Solvent Atoms	239
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	phasing