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Crystal structure of MMP-13 in complex with SC-78080
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.4 277 100mM Hepes buffer, pH 7.4
1.4M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.317 α = 92.42 b = 70.016 β = 94.23 c = 69.094 γ = 104.94
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 MAR CCD 165 mm Mirrors 2000-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.9 20 95 46273 -3 14.6
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 MOLECULAR REPLACEMENT THROUGHOUT 1.9 19.68 46273 2425 94.97 0.20879 0.2063 0.2189 0.25571 0.2618 RANDOM 14.852
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] 0.12 -0.09 0.29 -0.62 0.21 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.169 r_dihedral_angle_4_deg 21.101 r_dihedral_angle_3_deg 14.468 r_dihedral_angle_1_deg 6.113 r_scangle_it 2.006 r_scbond_it 1.264 r_angle_refined_deg 1.102 r_mcangle_it 0.88 r_angle_other_deg 0.798 r_mcbond_it 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.169 r_dihedral_angle_4_deg 21.101 r_dihedral_angle_3_deg 14.468 r_dihedral_angle_1_deg 6.113 r_scangle_it 2.006 r_scbond_it 1.264 r_angle_refined_deg 1.102 r_mcangle_it 0.88 r_angle_other_deg 0.798 r_mcbond_it 0.48 r_mcbond_other 0.093 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5189 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 156
Software Software Software Name Purpose MAR345 data collection X-PLOR model building REFMAC refinement DENZO data reduction SCALEPACK data scaling X-PLOR phasing