☰ Navigation Tabs
Crystal structure of Clostridium histolyticum ColH collagenase polycystic kidney-disease-like domain 2b at 1.4 Angstrom resolution in the presence of calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3JQU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 35% (w/v) PEG 5000, 0.2M ammonium sulfate, 0.1M MES pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.45 49.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.387 α = 90 b = 38.869 β = 98.43 c = 54.657 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 93 CCD ADSC QUANTUM 315r 2010-03-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID
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 1.42 22.19 96.7 0.039 33.1 3.5 37914 36663
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.42 1.44 85.8
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3JQU 1.42 22.19 37175 35993 1903 96.82 0.15223 0.15012 0.19133 0.1873 RANDOM 14.121
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.772 r_dihedral_angle_4_deg 24.216 r_dihedral_angle_3_deg 10.491 r_scangle_it 7.177 r_dihedral_angle_1_deg 6.448 r_scbond_it 5.405 r_mcangle_it 3.916 r_mcbond_it 2.882 r_rigid_bond_restr 2.771 r_angle_refined_deg 1.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 43.772 r_dihedral_angle_4_deg 24.216 r_dihedral_angle_3_deg 10.491 r_scangle_it 7.177 r_dihedral_angle_1_deg 6.448 r_scbond_it 5.405 r_mcangle_it 3.916 r_mcbond_it 2.882 r_rigid_bond_restr 2.771 r_angle_refined_deg 1.737 r_nbtor_refined 0.31 r_nbd_refined 0.213 r_chiral_restr 0.137 r_symmetry_vdw_refined 0.131 r_symmetry_hbond_refined 0.096 r_xyhbond_nbd_refined 0.083 r_metal_ion_refined 0.047 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1488 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 17
Software Software Software Name Purpose HKL-3000 data collection MLPHARE phasing REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling