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

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U2EPDB ENTRY 1U2E

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5277NANODROP, 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 coefficientSolvent content
2.0840.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.371α = 90
b = 46.371β = 90
c = 214.749γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102005-10-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.1ALS8.3.1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.729.34892.90.050.0511.76.228650
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)RedundancyNumber Unique Reflections (All)
11.71.7461.80.4050.4051.92.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1U2E1.729.3482864914491000.1470.1450.183RANDOM14.36
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]
0.350.180.35-0.53
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.568
r_dihedral_angle_4_deg21.224
r_dihedral_angle_3_deg11.741
r_dihedral_angle_1_deg6.579
r_scangle_it3.742
r_scbond_it2.751
r_mcangle_it1.977
r_angle_refined_deg1.561
r_mcbond_it1.454
r_angle_other_deg0.953
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.568
r_dihedral_angle_4_deg21.224
r_dihedral_angle_3_deg11.741
r_dihedral_angle_1_deg6.579
r_scangle_it3.742
r_scbond_it2.751
r_mcangle_it1.977
r_angle_refined_deg1.561
r_mcbond_it1.454
r_angle_other_deg0.953
r_mcbond_other0.402
r_symmetry_vdw_other0.254
r_nbd_refined0.223
r_nbd_other0.193
r_nbtor_refined0.188
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.165
r_symmetry_vdw_refined0.15
r_chiral_restr0.094
r_nbtor_other0.087
r_metal_ion_refined0.047
r_bond_refined_d0.016
r_bond_other_d0.008
r_gen_planes_refined0.007
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms2152
Nucleic Acid Atoms
Solvent Atoms314
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
MolProbitymodel building
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
MOLREPphasing