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NikR from Helicobacter pylori in closed trans-conformation and nickel bound to 2F, 2X and 2I 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 4.6 0.9-1.0 M NA-FORMATE, 0.1 M NA-CITRATE PH 4.0. CRYSTAL WAS SOAKED IN MOTHER LIQUOR WITH 30% GLYCEROL AND 0.1 M NICKEL SULFATE DURING ONE DAY.
Crystal Properties Matthews coefficient Solvent content 2.4 48.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.807 α = 90 b = 70.807 β = 90 c = 228.613 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 ID14-2 ESRF ID14-2
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 2.3 61.31 100 0.09 6.8 7.9 16035
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 2.3 2.42 100 0.47 1.6 8.2
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. 2.3 61.31 15156 795 100 0.204 0.202 0.2082 0.257 0.2671 RANDOM 30.29
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] 0.1 0.05 0.1 -0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.252 r_dihedral_angle_4_deg 18.686 r_dihedral_angle_3_deg 17.238 r_dihedral_angle_1_deg 7.349 r_scangle_it 2.995 r_scbond_it 1.94 r_mcangle_it 1.683 r_angle_refined_deg 1.586 r_angle_other_deg 1.231 r_mcbond_it 0.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.252 r_dihedral_angle_4_deg 18.686 r_dihedral_angle_3_deg 17.238 r_dihedral_angle_1_deg 7.349 r_scangle_it 2.995 r_scbond_it 1.94 r_mcangle_it 1.683 r_angle_refined_deg 1.586 r_angle_other_deg 1.231 r_mcbond_it 0.979 r_symmetry_vdw_other 0.245 r_chiral_restr 0.228 r_nbd_refined 0.21 r_nbd_other 0.188 r_symmetry_vdw_refined 0.171 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.166 r_symmetry_hbond_refined 0.153 r_nbtor_other 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 2107 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling