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Crystal structure of the catalytic domain of human MMP12 complexed with acetohydroxamic acid at atomic resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RMZ pdb entry 1RMZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293 Tris, PEG 6000, ACETOHYDROXAMIC ACID, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.913 α = 90 b = 59.552 β = 115.14 c = 53.497 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 MARRESEARCH double-crystal, Si(111) and Si(220) 2004-07-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 0.99993 ELETTRA 5.2R
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 1.02 48.4 97.6 0.057 0.057 5.5 3.7 70833 70833 6.63
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 1.02 1.08 84.9 0.251 0.251 2.7 3.1 8671
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 1RMZ 1.03 13.99 65283 65283 5517 100 0.1566 0.1566 0.15563 0.1562 0.16787 0.1677 RANDOM 8.688
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] 0.04 -0.12 0.09 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.082 r_dihedral_angle_4_deg 14.416 r_dihedral_angle_3_deg 11.832 r_dihedral_angle_1_deg 6.382 r_sphericity_free 3.907 r_scangle_it 3.254 r_sphericity_bonded 2.65 r_scbond_it 2.21 r_mcangle_it 1.635 r_angle_refined_deg 1.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.082 r_dihedral_angle_4_deg 14.416 r_dihedral_angle_3_deg 11.832 r_dihedral_angle_1_deg 6.382 r_sphericity_free 3.907 r_scangle_it 3.254 r_sphericity_bonded 2.65 r_scbond_it 2.21 r_mcangle_it 1.635 r_angle_refined_deg 1.379 r_mcbond_it 1.125 r_rigid_bond_restr 1.104 r_angle_other_deg 0.721 r_mcbond_other 0.523 r_nbd_refined 0.216 r_nbtor_refined 0.2 r_symmetry_vdw_other 0.199 r_nbd_other 0.185 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.146 r_xyhbond_nbd_refined 0.129 r_metal_ion_refined 0.11 r_nbtor_other 0.09 r_chiral_restr 0.075 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1238 Nucleic Acid Atoms Solvent Atoms 287 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing