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Crystal structure of yceI (HP1286) from Helicobacter pylori
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WUB PDB entry 1WUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 298 0.1M Tris-HCl, 2M Ammonium sulfate, pH 8.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.936 α = 90 b = 61.312 β = 92.88 c = 88.316 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 2009-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2.1 50.3 99.9 0.124 10.5 6.1 19367 19367 33.5
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 2.1 2.21 99.9 0.424 4.9 6 2823
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 1WUB 2.1 50.3 19367 19367 1519 99.89 0.21708 0.21708 0.21242 0.2305 0.27425 0.3033 RANDOM 7.54
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] 3.35 2.06 -1.27 -1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.696 r_dihedral_angle_4_deg 25.502 r_dihedral_angle_3_deg 18.491 r_dihedral_angle_1_deg 6.658 r_scangle_it 3.801 r_scbond_it 2.368 r_angle_refined_deg 1.921 r_mcangle_it 1.217 r_mcbond_it 0.665 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.696 r_dihedral_angle_4_deg 25.502 r_dihedral_angle_3_deg 18.491 r_dihedral_angle_1_deg 6.658 r_scangle_it 3.801 r_scbond_it 2.368 r_angle_refined_deg 1.921 r_mcangle_it 1.217 r_mcbond_it 0.665 r_chiral_restr 0.129 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_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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2632 Nucleic Acid Atoms Solvent Atoms 79 Heterogen Atoms 48
Software Software Software Name Purpose MAR345 data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling