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Crystal structure of Clostridium histolyticum colH collagenase collagen-binding domain 3 at 2 Angstrom resolution in presence of calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O8O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 PEG3350, Li2SO4, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.001 α = 90 b = 64.18 β = 90 c = 95.375 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 CCD ADSC QUANTUM 315 M SINGLE WAVELENGTH 2 1 CCD RIGAKU SATURN 92 Rigaku confocal
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97937 APS 19-ID 2 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2 28.5 99.4 0.086 16.8 18.8 24837 2 2
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 2 2.05 99.4 0.492 3.1 4.1 1792
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 2O8O 2 28.5 24835 1330 99.42 0.17736 0.17445 0.1757 0.23323 0.2332 RANDOM 25.598
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 38.42 r_dihedral_angle_4_deg 23.813 r_dihedral_angle_3_deg 15.188 r_dihedral_angle_1_deg 6.114 r_scangle_it 4.248 r_scbond_it 2.841 r_mcangle_it 1.946 r_angle_refined_deg 1.567 r_mcbond_it 1.151 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.42 r_dihedral_angle_4_deg 23.813 r_dihedral_angle_3_deg 15.188 r_dihedral_angle_1_deg 6.114 r_scangle_it 4.248 r_scbond_it 2.841 r_mcangle_it 1.946 r_angle_refined_deg 1.567 r_mcbond_it 1.151 r_nbtor_refined 0.317 r_nbd_refined 0.212 r_symmetry_vdw_refined 0.19 r_xyhbond_nbd_refined 0.159 r_chiral_restr 0.111 r_symmetry_hbond_refined 0.109 r_metal_ion_refined 0.108 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2801 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 6
Software Software Software Name Purpose HKL-3000 data collection PHASER phasing CCP4 model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling CCP4 phasing