☰ Navigation Tabs
Crystal structure of M-PMV DUTPASE relaxed end-product (dUMP) complex
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 41.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.682 α = 90 b = 60.682 β = 90 c = 63.544 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 MIRRORS 2004-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8031 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 1.84 52.56 98.3 0.041 17.1 2.9 11408 11408 -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 1.84 1.94 99.5 0.359 3.7 2.8 1679
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION RIGID BODY REFINEMENT THROUGHOUT PDB ENTRY 2D4L 1.84 20 10798 610 98.26 0.16885 0.16698 0.20113 0.2097 RANDOM 29.492
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] 1.34 0.67 1.34 -2.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.009 r_dihedral_angle_4_deg 16.925 r_dihedral_angle_3_deg 15.89 r_dihedral_angle_1_deg 11.668 r_scangle_it 7.581 r_scbond_it 5.302 r_mcangle_it 3.208 r_angle_refined_deg 1.994 r_mcbond_it 1.974 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.009 r_dihedral_angle_4_deg 16.925 r_dihedral_angle_3_deg 15.89 r_dihedral_angle_1_deg 11.668 r_scangle_it 7.581 r_scbond_it 5.302 r_mcangle_it 3.208 r_angle_refined_deg 1.994 r_mcbond_it 1.974 r_nbtor_refined 0.328 r_symmetry_hbond_refined 0.234 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.199 r_xyhbond_nbd_refined 0.193 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 803 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 20
Software Software Software Name Purpose MAR345 data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing