2RH0 | pdb_00002rh0

Crystal structure of NudC domain-containing protein 2 (13542905) from Mus musculus at 1.95 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	277	NANODROP, 0.2M NaNO3, 20.0% PEG 3350, No Buffer pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.568	α = 74.51
b = 64.504	β = 81.06
c = 64.423	γ = 81.22

Symmetry
Space Group	P 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	MARMOSAIC 300 mm CCD	Adjustable focusing mirrors in K-B geometry	2007-08-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.97942	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.95	29.148	95.5	0.096	0.096	3.1	2.9		47221			25.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.95	2	94.2		0.607	0.607	0.8	2.9	3450

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.95	29.148	47101	2394	95.33	0.192	0.19	0.2	0.235	0.24	RANDOM	28.349

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]
-0.35	0.8	1.24	-0.86	1.88	-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.194
r_dihedral_angle_3_deg	14.272
r_dihedral_angle_4_deg	13.768
r_scangle_it	7.946
r_scbond_it	5.49
r_dihedral_angle_1_deg	5.11
r_mcangle_it	3.508
r_mcbond_it	2.69
r_angle_refined_deg	1.61
r_angle_other_deg	0.896
r_mcbond_other	0.295
r_symmetry_vdw_other	0.276
r_nbd_refined	0.214
r_nbd_other	0.195
r_symmetry_hbond_refined	0.193
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.178
r_symmetry_vdw_refined	0.116
r_chiral_restr	0.099
r_nbtor_other	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4227
Nucleic Acid Atoms
Solvent Atoms	403
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing