2XMR

Crystal structure of human NDRG2 protein provides insight into its role as a tumor suppressor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
116% PEG 8000, 0.2 M CALCIUM ACETATE, 0.1 M MES (PH 6.8 TO 7.1)
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.232α = 90
b = 88.049β = 90
c = 126.907γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 6C1PAL/PLS6C1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
1230970.1411.274.6633292
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0792.20.441.833.1

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 2QMQ23060071321796.450.182820.180190.23247RANDOM28.606
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]
-0.45-0.10.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.103
r_dihedral_angle_4_deg18.423
r_dihedral_angle_3_deg15.297
r_dihedral_angle_1_deg8.966
r_scangle_it2.9
r_scbond_it1.845
r_angle_refined_deg1.342
r_mcangle_it1.245
r_mcbond_it0.76
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.103
r_dihedral_angle_4_deg18.423
r_dihedral_angle_3_deg15.297
r_dihedral_angle_1_deg8.966
r_scangle_it2.9
r_scbond_it1.845
r_angle_refined_deg1.342
r_mcangle_it1.245
r_mcbond_it0.76
r_nbtor_refined0.31
r_symmetry_hbond_refined0.276
r_symmetry_vdw_refined0.206
r_nbd_refined0.205
r_xyhbond_nbd_refined0.154
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6591
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing