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5'-Nucleotidase (E. coli) with an Engineered Disulfide Bridge (S228C, P513C)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HP1 PDB ENTRY 1HP1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 2.1 MALONATE PH 6.5
Crystal Properties Matthews coefficient Solvent content 2.7 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.132 α = 90 b = 83.132 β = 90 c = 180.664 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 2003-03-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR571
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 2.33 20 99.7 0.066 28.4 6.96 193519
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 2.33 2.41 100 0.165 11.8 6.84
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 1HP1 2.33 74.54 26420 1391 99.6 0.171 0.168 0.17 0.22 0.1605 RANDOM 27.94
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] -0.4 -0.4 0.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.628 r_scangle_it 4.119 r_scbond_it 2.575 r_angle_refined_deg 1.742 r_mcangle_it 1.685 r_mcbond_it 0.934 r_angle_other_deg 0.872 r_symmetry_vdw_refined 0.263 r_symmetry_vdw_other 0.254 r_nbd_other 0.253
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.628 r_scangle_it 4.119 r_scbond_it 2.575 r_angle_refined_deg 1.742 r_mcangle_it 1.685 r_mcbond_it 0.934 r_angle_other_deg 0.872 r_symmetry_vdw_refined 0.263 r_symmetry_vdw_other 0.254 r_nbd_other 0.253 r_nbd_refined 0.206 r_xyhbond_nbd_refined 0.188 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.102 r_nbtor_other 0.088 r_bond_refined_d 0.024 r_gen_planes_refined 0.008 r_gen_planes_other 0.005 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 4048 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing