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Crystal structure of human CTBP2 dehydrogenase complexed with NAD(H)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MX3 PDB entries 1MX3, 1HL3 experimental model PDB 1HL3 PDB entries 1MX3, 1HL3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.2M KSCN, 0.1M BIS-TRIS PROPANE, 20% PEG3350, 10% ETHYLENE GLYCOL, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.84 56.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.754 α = 90 b = 141.574 β = 98.93 c = 138.215 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2006-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99991 SLS X10SA
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 2.77 43.31 100 0.148 0.162 11.6 6.1 84796 2
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 2.77 2.92 100 0.81 0.89 2 5.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 entries 1MX3, 1HL3 2.8 43.31 2 84796 78004 4104 99.98 0.2098 0.20733 0.213 0.25736 0.259 RANDOM 40.724
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] 1.63 -0.55 -4.83 3.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.744 r_dihedral_angle_3_deg 17.854 r_dihedral_angle_4_deg 17.542 r_dihedral_angle_1_deg 6.348 r_scangle_it 2.014 r_angle_refined_deg 1.458 r_scbond_it 1.253 r_angle_other_deg 1.116 r_mcangle_it 0.548 r_mcbond_it 0.349
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.744 r_dihedral_angle_3_deg 17.854 r_dihedral_angle_4_deg 17.542 r_dihedral_angle_1_deg 6.348 r_scangle_it 2.014 r_angle_refined_deg 1.458 r_scbond_it 1.253 r_angle_other_deg 1.116 r_mcangle_it 0.548 r_mcbond_it 0.349 r_symmetry_hbond_refined 0.27 r_nbd_refined 0.211 r_nbd_other 0.195 r_nbtor_refined 0.184 r_symmetry_vdw_refined 0.181 r_symmetry_vdw_other 0.178 r_xyhbond_nbd_refined 0.149 r_mcbond_other 0.128 r_nbtor_other 0.087 r_chiral_restr 0.075 r_xyhbond_nbd_other 0.023 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_metal_ion_refined 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 20223 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 352
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling PHASER phasing