2QMQ

Crystal structure of a n-myc downstream regulated 2 protein (ndrg2, syld, ndr2, ai182517, au040374) from mus musculus at 1.70 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1U2E	PDB ENTRY 1U2E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	277	NANODROP, 20.0% PEG 400, 0.2M MgCl2, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 7.50

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.371	α = 90
b = 46.371	β = 90
c = 214.749	γ = 120

Symmetry
Space Group	P 31 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		2005-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

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	1.7	29.348	92.9	0.05	0.05	11.7	6.2		28650

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	1.7	1.74	61.8		0.405	0.405	1.9	2.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1U2E	1.7	29.348	28649	1449	100	0.147	0.145	0.183	RANDOM	14.36

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	0.18		0.35		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.568
r_dihedral_angle_4_deg	21.224
r_dihedral_angle_3_deg	11.741
r_dihedral_angle_1_deg	6.579
r_scangle_it	3.742
r_scbond_it	2.751
r_mcangle_it	1.977
r_angle_refined_deg	1.561
r_mcbond_it	1.454
r_angle_other_deg	0.953
r_mcbond_other	0.402
r_symmetry_vdw_other	0.254
r_nbd_refined	0.223
r_nbd_other	0.193
r_nbtor_refined	0.188
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.165
r_symmetry_vdw_refined	0.15
r_chiral_restr	0.094
r_nbtor_other	0.087
r_metal_ion_refined	0.047
r_bond_refined_d	0.016
r_bond_other_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2152
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing