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Crystal structure of a n-myc downstream regulated 2 protein (ndrg2, syld, ndr2, ai182517, au040374) from mus musculus at 1.70 A resolution
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 (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) 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 0.1562 0.183 0.1927 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
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