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Crystal structure of putative lipoprotein from Peptoclostridium difficile 630 (fragment)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.09 M Malonic Acid, 0.013 M Ammonium Citrate Tribasic, 0.006 M Succinic Acid, 0.015 M DL-Malic Acid, 0.02 M Sodium Acetate, 0.025 M Sodium Formate, 0.008 M Ammonium Tartrate Dibasic, 0.1 M HEPES:NaOH pH 7.0, 10% (w/v) PEG MME 5000, cryo 25% glycerol
Crystal Properties Matthews coefficient Solvent content 2.49 50.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.755 α = 90 b = 119.501 β = 90 c = 185.912 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 100 CCD ADSC QUANTUM 315r mirrors 2013-08-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97915 APS 19-ID
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 1.98 30 96.8 0.123 12.4 4.8 57544 -3
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 1.98 2.01 97 0.848 2.25 4.7
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 SAD THROUGHOUT 1.98 30 56177 1077 95.89 0.18067 0.17981 0.1875 0.22628 0.2361 THIN SHELLS 39.857
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] 0.85 -0.44 -0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.244 r_dihedral_angle_4_deg 22.16 r_dihedral_angle_3_deg 15.312 r_long_range_B_refined 8.013 r_long_range_B_other 8.013 r_scangle_other 6.085 r_dihedral_angle_1_deg 4.669 r_scbond_it 3.89 r_scbond_other 3.89 r_mcangle_other 3.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.244 r_dihedral_angle_4_deg 22.16 r_dihedral_angle_3_deg 15.312 r_long_range_B_refined 8.013 r_long_range_B_other 8.013 r_scangle_other 6.085 r_dihedral_angle_1_deg 4.669 r_scbond_it 3.89 r_scbond_other 3.89 r_mcangle_other 3.388 r_mcangle_it 3.387 r_mcbond_it 2.244 r_mcbond_other 2.234 r_angle_refined_deg 1.457 r_angle_other_deg 0.802 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5676 Nucleic Acid Atoms Solvent Atoms 353 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling Auto-Rickshaw phasing