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5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (P90C, L424C)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HO5 PDB ENTRY 1HO5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 1.8 M LI2SO4, 100MM TRIS, 1MM MNCL, 10 MM BETAINE, 10% 2-METHYL-2,4-PENTANDIOLE, pH 8.00
Crystal Properties Matthews coefficient Solvent content 3.2 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.689 α = 90 b = 97.689 β = 90 c = 312.051 γ = 90
Symmetry Space Group P 41 21 2
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 MARRESEARCH MIRRORS, TRIANGULAR MONOCHROMATOR 2002-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
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 2.1 30 95.1 0.069 17.2 3.2 89316
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) 1 2.1 2.18 95.6 0.267 4.7 3.3
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 PDB ENTRY 1HO5 2.1 19.96 80645 4255 95.3 0.159 0.156 0.1748 0.205 0.169 RANDOM 22.26
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] 0.03 0.03 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.581 r_scangle_it 4.709 r_scbond_it 2.933 r_mcangle_it 1.754 r_angle_refined_deg 1.743 r_mcbond_it 0.97 r_angle_other_deg 0.922 r_symmetry_vdw_other 0.291 r_nbd_other 0.252 r_symmetry_hbond_refined 0.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.581 r_scangle_it 4.709 r_scbond_it 2.933 r_mcangle_it 1.754 r_angle_refined_deg 1.743 r_mcbond_it 0.97 r_angle_other_deg 0.922 r_symmetry_vdw_other 0.291 r_nbd_other 0.252 r_symmetry_hbond_refined 0.239 r_nbd_refined 0.208 r_xyhbond_nbd_refined 0.201 r_symmetry_vdw_refined 0.181 r_chiral_restr 0.114 r_nbtor_other 0.089 r_bond_refined_d 0.022 r_gen_planes_other 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8194 Nucleic Acid Atoms Solvent Atoms 916 Heterogen Atoms 22
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing BEAST phasing REFMAC refinement