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Structure of futalosine hydrolase mutant of Helicobacter pylori strain 26695
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BMX PDB ENTRY 4BMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M BIS-TRIS PH 5.5, 25% PEG-3350, 0.2 M MGCL2.6H2O
Crystal Properties Matthews coefficient Solvent content 2.02 39.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.445 α = 90 b = 67.746 β = 104.96 c = 100.089 γ = 90
Symmetry Space Group I 1 2 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 PIXEL DECTRIS PILATUS 6M M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.79 55.48 98.4 0.05 15.8 4.2 40405 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 1.79 1.83 99 0.62 2 4.3
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 4BMX 1.79 55.55 38371 2031 98.26 0.18343 0.18161 0.1811 0.216 0.2159 RANDOM 28.446
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] 0.23 0.29 -0.26 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.915 r_dihedral_angle_4_deg 15.67 r_dihedral_angle_3_deg 13.509 r_dihedral_angle_1_deg 5.799 r_scbond_it 2.679 r_mcangle_it 2.228 r_angle_refined_deg 1.843 r_mcbond_it 1.719 r_chiral_restr 0.132 r_bond_refined_d 0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.915 r_dihedral_angle_4_deg 15.67 r_dihedral_angle_3_deg 13.509 r_dihedral_angle_1_deg 5.799 r_scbond_it 2.679 r_mcangle_it 2.228 r_angle_refined_deg 1.843 r_mcbond_it 1.719 r_chiral_restr 0.132 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it 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 3465 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing