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Crystal structure of the N-terminally His6-tagged HP0902, an uncharacterized protein from Helicobacter pylori 26695
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q30
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 PEG 3350, sodium chloride, Tris-HCl
Crystal Properties Matthews coefficient Solvent content 1.91 35.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.512 α = 90 b = 78.643 β = 112.22 c = 41.404 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 270 2010-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 1.4 71 99.8 0.054 15.8 6.4 38998
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 FREE R-VALUE 2q30 1.4 19.85 37000 1952 99.77 0.18211 0.18076 0.1808 0.20779 0.2078 RANDOM 19.028
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] -0.03 0.07 -0.08 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.085 r_dihedral_angle_4_deg 20.972 r_dihedral_angle_3_deg 14.164 r_scangle_it 7.853 r_dihedral_angle_1_deg 7.409 r_scbond_it 4.567 r_mcangle_it 2.758 r_angle_refined_deg 2.367 r_mcbond_it 1.51 r_chiral_restr 0.164
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.085 r_dihedral_angle_4_deg 20.972 r_dihedral_angle_3_deg 14.164 r_scangle_it 7.853 r_dihedral_angle_1_deg 7.409 r_scbond_it 4.567 r_mcangle_it 2.758 r_angle_refined_deg 2.367 r_mcbond_it 1.51 r_chiral_restr 0.164 r_bond_refined_d 0.03 r_gen_planes_refined 0.012 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_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 1516 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data processing SCALA data scaling MOLREP phasing SHELXDE model building MOSFLM data reduction