1RMZ

Crystal structure of the catalytic domain of human MMP12 complexed with the inhibitor NNGH at 1.3 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OS9pdb entry 1OS9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293Tris, PEG6000, NNGH, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2645.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.194α = 90
b = 62.564β = 90
c = 37.262γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHdouble-crystal monochromator Si(111) and Si(220)2003-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R1.20000ELETTRA5.2R

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.3446.40798.40.0570.0577.26.2362953629516.389
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)RedundancyNumber Unique Reflections (All)
1.341.4192.60.3080.3082.34.84889

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1OS91.3420336783367825781000.181110.181110.178570.2149RANDOM18.214
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]
-1.38-0.722.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.416
r_sphericity_free3.899
r_scangle_it3.53
r_sphericity_bonded3.012
r_scbond_it2.461
r_mcangle_it2.067
r_angle_refined_deg1.668
r_mcbond_it1.373
r_rigid_bond_restr1.352
r_angle_other_deg1.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.416
r_sphericity_free3.899
r_scangle_it3.53
r_sphericity_bonded3.012
r_scbond_it2.461
r_mcangle_it2.067
r_angle_refined_deg1.668
r_mcbond_it1.373
r_rigid_bond_restr1.352
r_angle_other_deg1.006
r_symmetry_vdw_other0.284
r_nbd_other0.246
r_symmetry_vdw_refined0.221
r_nbd_refined0.217
r_symmetry_hbond_refined0.217
r_chiral_restr0.197
r_xyhbond_nbd_refined0.181
r_metal_ion_refined0.107
r_nbtor_other0.087
r_bond_refined_d0.014
r_gen_planes_refined0.01
r_gen_planes_other0.009
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1246
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing