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Crystal structure analysis of HP1043, an orphan resonse regulator of h. pylori
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 PEG 8K 3%, 100MM MES, 200MM CA-CACODYLATE, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.86 34.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.967 α = 90 b = 41.311 β = 90 c = 31.689 γ = 90
Symmetry Space Group P 21 21 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 BRUKER PROTEUM 300 2005-05-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6B 0.97940, 0.97952, 0.97962, 0.98742 PAL/PLS 6B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 50 99.9 0.099 7.3 11373
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 100 0.368 7.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.8 44.5 10781 543 99.6 0.208 0.206 0.2054 0.24 0.2351 RANDOM 21.15
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] -1.12 -0.99 2.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.675 r_dihedral_angle_4_deg 19.062 r_dihedral_angle_3_deg 14.64 r_sphericity_free 6.178 r_dihedral_angle_1_deg 5.433 r_scangle_it 4.617 r_scbond_it 3.563 r_sphericity_bonded 3.007 r_rigid_bond_restr 2.657 r_mcangle_it 2.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.675 r_dihedral_angle_4_deg 19.062 r_dihedral_angle_3_deg 14.64 r_sphericity_free 6.178 r_dihedral_angle_1_deg 5.433 r_scangle_it 4.617 r_scbond_it 3.563 r_sphericity_bonded 3.007 r_rigid_bond_restr 2.657 r_mcangle_it 2.189 r_mcbond_it 1.564 r_angle_refined_deg 1.461 r_symmetry_vdw_refined 0.314 r_nbtor_refined 0.302 r_nbd_refined 0.218 r_symmetry_hbond_refined 0.184 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 925 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms
Software Software Software Name Purpose SOLVE phasing REFMAC refinement HKL-2000 data collection DENZO data reduction SCALEPACK data scaling