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apo-NIKR from helicobacter pylori in closed trans-conformation
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 4.8 0.9-1 M NA-FORMATE, O.1 M NA-CITRATE PH 4
Crystal Properties Matthews coefficient Solvent content 2.4 49.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.055 α = 90 b = 71.055 β = 90 c = 229.023 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 ID14-1 ESRF ID14-1
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 2.05 61.55 99.6 0.08 8 5.4 24159 24.8
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 2.05 2.16 99.6 0.44 1.7 5.5
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 NIKR FROM HELICOBACTER PYLORI SOLVED BY SAD METHOD USING MERCURY DERIVATIVE. 2.05 61.55 21171 1140 99.3 0.201 0.199 0.1976 0.25 0.2476 RANDOM 29.66
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.215 r_dihedral_angle_4_deg 22.545 r_dihedral_angle_3_deg 17.517 r_dihedral_angle_1_deg 6.913 r_scangle_it 5.163 r_scbond_it 3.34 r_mcangle_it 2.338 r_angle_refined_deg 1.673 r_mcbond_it 1.518 r_symmetry_hbond_refined 0.343
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.215 r_dihedral_angle_4_deg 22.545 r_dihedral_angle_3_deg 17.517 r_dihedral_angle_1_deg 6.913 r_scangle_it 5.163 r_scbond_it 3.34 r_mcangle_it 2.338 r_angle_refined_deg 1.673 r_mcbond_it 1.518 r_symmetry_hbond_refined 0.343 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.245 r_nbd_refined 0.232 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.134 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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_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 2171 Nucleic Acid Atoms Solvent Atoms 127 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling