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New crystal form of the C-terminal domain of Helicobacter pylori MotB (residues 125-256)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CYP PDB ENTRY 3CYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 15% PEG3350, 200mM sodium tartrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.66 53.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.56 α = 90 b = 100.336 β = 119.51 c = 108.49 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 MARMOSAIC 225 mm CCD 2007-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.9 SLS X06SA
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 2.5 15 99 0.105 10.4 69194
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 2.5 2.64 99 0.363 2.8
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 3CYP 2.5 15 69176 3498 99.47 0.189 0.186 0.1843 0.249 0.2445 RANDOM 51.788
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] 0.92 1.25 -0.7 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.241 r_dihedral_angle_3_deg 17.964 r_dihedral_angle_4_deg 17.276 r_dihedral_angle_1_deg 6.062 r_scangle_it 2.822 r_scbond_it 1.89 r_angle_refined_deg 1.429 r_mcangle_it 1.191 r_mcbond_it 0.708 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.241 r_dihedral_angle_3_deg 17.964 r_dihedral_angle_4_deg 17.276 r_dihedral_angle_1_deg 6.062 r_scangle_it 2.822 r_scbond_it 1.89 r_angle_refined_deg 1.429 r_mcangle_it 1.191 r_mcbond_it 0.708 r_nbtor_refined 0.312 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.217 r_symmetry_hbond_refined 0.195 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12781 Nucleic Acid Atoms Solvent Atoms 433 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling AMoRE phasing