5O1W

Structure of Nrd1 RNA binding domain

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		291	12% PEG 8000, 0.1 M Bicine pH 9

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.991	α = 90
b = 60.991	β = 90
c = 157.958	γ = 90

Symmetry
Space Group	P 43 21 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	PIXEL	DECTRIS PILATUS3 2M		2015-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.976250	ESRF	ID23-2

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	2.3	48.14	99.1	32.1	24.5	13708	383024

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.3	56.9	13317	698	99.96	0.20796	0.2068	0.23297	RANDOM	59.946

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]
2.14			2.14		-4.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.786
r_dihedral_angle_4_deg	22.598
r_dihedral_angle_3_deg	13.334
r_long_range_B_refined	7.906
r_long_range_B_other	7.906
r_dihedral_angle_1_deg	6.816
r_scangle_other	3.573
r_mcangle_it	2.909
r_mcangle_other	2.908
r_scbond_it	2.144
r_scbond_other	2.132
r_mcbond_it	1.761
r_mcbond_other	1.761
r_angle_refined_deg	1.306
r_angle_other_deg	0.906
r_chiral_restr	0.078
r_bond_refined_d	0.01
r_gen_planes_refined	0.005
r_bond_other_d	0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1327
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Coot	model building
XDS	data scaling
SHELX	phasing