☰ Navigation Tabs
CRYSTAL STRUCTURE OF M-PMV DUTPASE - DUPNPP complex revealing distorted ligand geometry (approach intermediate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2D4L PDB entry 2D4L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 PEG 8000, AMMONIUM CHLORIDE, TRIS, PH 8.5, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.619 α = 90 b = 60.619 β = 90 c = 63.731 γ = 120
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 MAR CCD 165 mm BENT, VERTICALLY FOCUSING MIRROR 2005-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8034 EMBL/DESY, HAMBURG X13
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.65 20 98.4 0.056 21 2.9 15827 15827 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.73 99.2 0.262 4.3 2.5 2107
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 rigid body refinement THROUGHOUT PDB entry 2D4L 1.65 20 15826 14973 853 98.44 0.1683 0.1668 0.1816 0.1945 0.2082 RANDOM 26.6316
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] 0.67 0.34 0.67 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.366 r_dihedral_angle_4_deg 27.458 r_dihedral_angle_3_deg 11.317 r_scangle_it 8.845 r_scbond_it 6.526 r_dihedral_angle_1_deg 6.206 r_mcangle_it 5.223 r_mcbond_it 4.827 r_angle_refined_deg 2.196 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.366 r_dihedral_angle_4_deg 27.458 r_dihedral_angle_3_deg 11.317 r_scangle_it 8.845 r_scbond_it 6.526 r_dihedral_angle_1_deg 6.206 r_mcangle_it 5.223 r_mcbond_it 4.827 r_angle_refined_deg 2.196 r_nbtor_refined 0.327 r_symmetry_vdw_refined 0.24 r_nbd_refined 0.239 r_symmetry_hbond_refined 0.219 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.128 r_metal_ion_refined 0.026 r_bond_refined_d 0.018 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 828 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection XDS data reduction XSCALE data scaling REFMAC phasing