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Native structure of futalosine hydrolase of Helicobacter pylori strain 26695
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NM4 PDB ENTRY 3NM4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 PROTEIN WAS CRYSTALLIZED IN 4.0 M NA/K PHOSPHATE
Crystal Properties Matthews coefficient Solvent content 2.67 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.314 α = 90 b = 90.573 β = 90 c = 108.381 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.76 54.19 98 0.13 15.8 10.1 57414 6
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 1.76 1.79 96.9 0.93 2.2 7.5
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 3NM4 1.76 54.249 57357 2855 97.752 0.171 0.1687 0.1683 0.2118 0.212 RANDOM 20.842
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] 0.164 -0.005 -0.159
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.86 r_dihedral_angle_4_deg 17.573 r_dihedral_angle_3_deg 12.925 r_dihedral_angle_1_deg 6.005 r_scangle_it 4.294 r_scbond_it 2.89 r_mcangle_it 2.015 r_angle_refined_deg 1.986 r_mcbond_it 1.471 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.86 r_dihedral_angle_4_deg 17.573 r_dihedral_angle_3_deg 12.925 r_dihedral_angle_1_deg 6.005 r_scangle_it 4.294 r_scbond_it 2.89 r_mcangle_it 2.015 r_angle_refined_deg 1.986 r_mcbond_it 1.471 r_nbtor_refined 0.316 r_nbd_refined 0.238 r_chiral_restr 0.162 r_xyhbond_nbd_refined 0.136 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 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_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 3471 Nucleic Acid Atoms Solvent Atoms 363 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing