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NikR from Helicobacter pylori in closed trans-conformation and nickel bound to 4 intermediary sites
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other NIKR FROM HELICOBACTER PYLORI SOLVED BY SAD METHOD USING MERCURY DERIVATIVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 0.9-1.0 M NA-FORMATE, 0.1M NA-CITRATE PH 4.0. CRYSTAL WAS SOAKED IN MOTHER LIQUOR WITH 30% GLYCEROL AND 0.02 M NICKEL CHLORIDE DURING ONE HOUR.
Crystal Properties Matthews coefficient Solvent content 2.5 49.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.598 α = 90 b = 71.598 β = 90 c = 228.834 γ = 120
Symmetry Space Group P 61 2 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 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 62.02 99.7 0.07 8.4 7.4 15378
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 2.35 2.48 99.7 0.49 1.6 6.7
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 NIKR FROM HELICOBACTER PYLORI SOLVED BY SAD METHOD USING MERCURY DERIVATIVE 2.35 62.02 14496 788 99.7 0.232 0.23 0.2354 0.282 0.294 RANDOM 41.68
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 -0.12 -0.23 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.57 r_dihedral_angle_4_deg 20.427 r_dihedral_angle_3_deg 17.228 r_dihedral_angle_1_deg 7.334 r_scangle_it 4.135 r_scbond_it 2.477 r_mcangle_it 1.996 r_angle_refined_deg 1.643 r_mcbond_it 1.19 r_angle_other_deg 0.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.57 r_dihedral_angle_4_deg 20.427 r_dihedral_angle_3_deg 17.228 r_dihedral_angle_1_deg 7.334 r_scangle_it 4.135 r_scbond_it 2.477 r_mcangle_it 1.996 r_angle_refined_deg 1.643 r_mcbond_it 1.19 r_angle_other_deg 0.866 r_symmetry_vdw_refined 0.323 r_symmetry_vdw_other 0.322 r_nbd_refined 0.214 r_nbd_other 0.195 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.186 r_mcbond_other 0.185 r_nbtor_refined 0.173 r_nbtor_other 0.092 r_chiral_restr 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_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 2085 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling