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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 2.12 41.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.884 α = 90 b = 60.884 β = 90 c = 63.867 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 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2005-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B 0.8430 EMBL/DESY, HAMBURG BW7B
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 2 20 97.8 0.06 11.7 2.4 8979 8979 -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 2 2.1 98.7 0.493 2.6 2.4 1239
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 2 20 8493 8493 482 97.86 0.16473 0.16241 0.1666 0.20407 0.2129 RANDOM 34.695
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] 1.81 0.91 1.81 -2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.512 r_dihedral_angle_4_deg 31.503 r_dihedral_angle_3_deg 16.126 r_scangle_it 10.286 r_scbond_it 7.393 r_dihedral_angle_1_deg 7.188 r_mcangle_it 2.656 r_angle_refined_deg 1.885 r_mcbond_it 1.527 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.512 r_dihedral_angle_4_deg 31.503 r_dihedral_angle_3_deg 16.126 r_scangle_it 10.286 r_scbond_it 7.393 r_dihedral_angle_1_deg 7.188 r_mcangle_it 2.656 r_angle_refined_deg 1.885 r_mcbond_it 1.527 r_nbtor_refined 0.32 r_nbd_refined 0.228 r_symmetry_vdw_refined 0.225 r_xyhbond_nbd_refined 0.196 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.121 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 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 814 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 20
Software Software Software Name Purpose MAR345 data collection REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing