2XMQ

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
19% PEG 8000, 0.2 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE (PH 6.4 TO 7.5).
Crystal Properties
Matthews coefficientSolvent content
2.755

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.411α = 90
b = 88.897β = 90
c = 126.799γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 4APAL/PLS4A

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
12.814099.60.119.16.6243612
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)
12.82.9990.424.56.3

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 2QMQ2.814023070124299.190.20390.200950.25847RANDOM41.372
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]
-0.11-1.111.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.244
r_dihedral_angle_4_deg25.877
r_dihedral_angle_3_deg21.222
r_dihedral_angle_1_deg9.456
r_scangle_it3.501
r_scbond_it2.371
r_angle_refined_deg2.332
r_mcangle_it1.833
r_mcbond_it1.114
r_nbtor_refined0.338
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.244
r_dihedral_angle_4_deg25.877
r_dihedral_angle_3_deg21.222
r_dihedral_angle_1_deg9.456
r_scangle_it3.501
r_scbond_it2.371
r_angle_refined_deg2.332
r_mcangle_it1.833
r_mcbond_it1.114
r_nbtor_refined0.338
r_symmetry_vdw_refined0.324
r_symmetry_hbond_refined0.316
r_nbd_refined0.26
r_xyhbond_nbd_refined0.186
r_chiral_restr0.137
r_bond_refined_d0.029
r_gen_planes_refined0.008
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 Atoms6615
Nucleic Acid Atoms
Solvent Atoms93
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing