3CTR | pdb_00003ctr

Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	293	2 M LiSO4, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.107	α = 90
b = 81.107	β = 90
c = 78.058	γ = 90

Symmetry
Space Group	I 41 2 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	MAR CCD 165 mm	mirrors	2007-03-28	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	MAR CCD 165 mm	mirrors	2007-04-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	1.078	EMBL/DESY, HAMBURG	BW7A
2	SYNCHROTRON	BESSY BEAMLINE 14.2	0.9778, 0.97861, 0.91841	BESSY	14.2

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
1,2	2.1	30	99.9	0.038	67.9	13.6	7925	7918	2	3

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	2.1	2.18	100		0.202	14.4	7.8	776

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2.1	15	7466	7448	382	99.76	0.21124	0.21124	0.20959	0.21	0.24287	0.24	RANDOM	45.363

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]
-1.83			-1.83		3.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.777
r_dihedral_angle_4_deg	15.778
r_dihedral_angle_3_deg	13.823
r_dihedral_angle_1_deg	6.203
r_scangle_it	3.207
r_scbond_it	2.007
r_mcangle_it	1.51
r_angle_refined_deg	1.287
r_mcbond_it	0.876
r_nbtor_refined	0.303
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.154
r_xyhbond_nbd_refined	0.145
r_symmetry_hbond_refined	0.13
r_chiral_restr	0.097
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	602
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	33

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXCD	phasing
SHELXE	model building