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Human MMP-8 in complex with peptide IAG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BZS pdb entry 1BZS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.1M Tris-HCl, 20% PEG3350, 200mM acetohydroxamic acid, 0.2M MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.38 48.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.207 α = 90 b = 68.533 β = 98.1 c = 78.281 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 100 CCD MARRESEARCH Fixed exit double crystal Si [111], horizontally focussing 2006-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.5 38.75 100 0.082 0.082 6.6 6.7 55607 55607 10.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.58 100 0.314 0.314 2.2 6 8108
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 (All) 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 pdb entry 1BZS 1.5 38.75 50507 50507 5098 100 0.1664 0.1664 0.16375 0.164 0.19237 0.193 RANDOM 12.388
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] -0.14 -0.05 -0.35 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.625 r_dihedral_angle_4_deg 16.734 r_dihedral_angle_3_deg 12.546 r_dihedral_angle_1_deg 5.785 r_scangle_it 2.815 r_sphericity_free 2.587 r_scbond_it 2.291 r_rigid_bond_restr 2.179 r_sphericity_bonded 1.716 r_mcangle_it 1.275
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.625 r_dihedral_angle_4_deg 16.734 r_dihedral_angle_3_deg 12.546 r_dihedral_angle_1_deg 5.785 r_scangle_it 2.815 r_sphericity_free 2.587 r_scbond_it 2.291 r_rigid_bond_restr 2.179 r_sphericity_bonded 1.716 r_mcangle_it 1.275 r_angle_refined_deg 1.119 r_mcbond_it 0.762 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.255 r_nbd_refined 0.193 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.115 r_metal_ion_refined 0.088 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2516 Nucleic Acid Atoms Solvent Atoms 565 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction CCP4 data scaling MOLREP phasing