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Crystal Structure of Tip-Alpha N34 (HP0596) from Helicobacter pylori at pH8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WCQ PDB ENTRY 2WCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 100 MM TRIS PH 8.5, 26% PEG4000, 50 MM MGCL2
Crystal Properties Matthews coefficient Solvent content 2 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.88 α = 90 b = 67.26 β = 90 c = 97.47 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 CCD ADSC CCD MIRRORS 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 1.7 27.68 99.3 0.04 10.76 3.57 35854 2 26.4
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 1.7 1.79 99.6 0.41 1.9 3.6
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 2WCQ 1.7 55.38 34065 1788 99.2 0.184 0.182 0.2111 0.22 0.2465 RANDOM 12.36
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] 1.11 -0.87 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.589 r_dihedral_angle_4_deg 18.738 r_dihedral_angle_3_deg 14.335 r_dihedral_angle_1_deg 5.64 r_scangle_it 4.513 r_scbond_it 2.744 r_mcangle_it 1.574 r_angle_refined_deg 1.52 r_angle_other_deg 0.995 r_mcbond_it 0.895
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.589 r_dihedral_angle_4_deg 18.738 r_dihedral_angle_3_deg 14.335 r_dihedral_angle_1_deg 5.64 r_scangle_it 4.513 r_scbond_it 2.744 r_mcangle_it 1.574 r_angle_refined_deg 1.52 r_angle_other_deg 0.995 r_mcbond_it 0.895 r_mcbond_other 0.283 r_chiral_restr 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.001 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_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 2354 Nucleic Acid Atoms Solvent Atoms 354 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing