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Crystal structure of the catalytic domain of human matrix metalloproteinase 10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G49 PDB entry 1G49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Tris-HCl, PEG 6000, Acetohydroxamic acid, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.09 41.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.152 α = 90 b = 61.141 β = 108.68 c = 68.588 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 4 Si(111) 2003-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9330 ESRF ID29
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 2.1 20 0.14 0.14 3.6 3 25246
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) 2.1 2.21 89.1 0.38 0.38 1.8 2.1
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1G49 2.1 51.3 21809 1962 100 0.27785 0.27599 0.2702 0.29797 RANDOM 37.771
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] -2.75 -0.38 0.87 1.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 10.558 r_scangle_it 2.328 r_angle_refined_deg 2.247 r_scbond_it 1.408 r_mcangle_it 1.251 r_mcbond_it 0.656 r_symmetry_vdw_refined 0.362 r_nbd_refined 0.297 r_xyhbond_nbd_refined 0.252 r_symmetry_hbond_refined 0.241
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 10.558 r_scangle_it 2.328 r_angle_refined_deg 2.247 r_scbond_it 1.408 r_mcangle_it 1.251 r_mcbond_it 0.656 r_symmetry_vdw_refined 0.362 r_nbd_refined 0.297 r_xyhbond_nbd_refined 0.252 r_symmetry_hbond_refined 0.241 r_chiral_restr 0.199 r_metal_ion_refined 0.165 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 3746 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 78
Software Software Software Name Purpose REFMAC refinement SCALA data scaling MOLREP phasing CNS refinement CCP4 data scaling MOSFLM data reduction