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Crystal structure of Clostridium histolyticum colg collagenase PKD domain 2 at 1.6 Angstrom resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C4X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 277 MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.13 42.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.95 α = 90 b = 48.992 β = 90 c = 70.858 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 113 CCD RIGAKU SATURN 92 2008-04-05 M SINGLE WAVELENGTH 2 1 x-ray 93 CCD ADSC QUANTUM 315 2008-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5478 2 SYNCHROTRON APS BEAMLINE 19-BM 0.919457 APS 19-BM
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 1.6 37.9 99.9 0.061 30.9 4.1 39924 39884
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 1.58 1.69 99.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2C4X 1.6 37.9 20556 20159 1092 99.9 0.1782 0.17649 0.1758 0.20951 0.2087 RANDOM 20.237
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] 0.49 -0.29 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.237 r_dihedral_angle_4_deg 21.012 r_dihedral_angle_3_deg 15.157 r_scangle_it 6.166 r_dihedral_angle_1_deg 5.557 r_scbond_it 3.795 r_mcangle_it 2.492 r_angle_refined_deg 2.042 r_mcbond_it 1.479 r_chiral_restr 0.166
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.237 r_dihedral_angle_4_deg 21.012 r_dihedral_angle_3_deg 15.157 r_scangle_it 6.166 r_dihedral_angle_1_deg 5.557 r_scbond_it 3.795 r_mcangle_it 2.492 r_angle_refined_deg 2.042 r_mcbond_it 1.479 r_chiral_restr 0.166 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1290 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 1
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