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dCTP deaminase-dUTPase from Bacillus halodurans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 300 200 mM lithium citrate, 20% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.06 40.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.72 α = 90 b = 55.63 β = 97.36 c = 95.6 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 MAR CCD 165 mm 2010-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 1.03796 MAX II I911-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.35 95 98.8 0.164 8.87 3.27 40236
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.35 2.64 0.761
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 2QXX 2.35 94.81 38223 2013 98.84 0.20901 0.20716 0.2111 0.24385 0.247 RANDOM 32.59
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] 1.97 1.29 -2.73 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.572 r_dihedral_angle_4_deg 22.014 r_dihedral_angle_3_deg 13.566 r_dihedral_angle_1_deg 6.392 r_long_range_B_refined 5.181 r_long_range_B_other 5.145 r_scangle_other 2.595 r_mcangle_it 1.981 r_mcangle_other 1.981 r_angle_refined_deg 1.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.572 r_dihedral_angle_4_deg 22.014 r_dihedral_angle_3_deg 13.566 r_dihedral_angle_1_deg 6.392 r_long_range_B_refined 5.181 r_long_range_B_other 5.145 r_scangle_other 2.595 r_mcangle_it 1.981 r_mcangle_other 1.981 r_angle_refined_deg 1.625 r_scbond_it 1.611 r_scbond_other 1.61 r_angle_other_deg 1.41 r_mcbond_it 1.192 r_mcbond_other 1.191 r_chiral_restr 0.081 r_bond_refined_d 0.011 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8359 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 187
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing