1Y93

Crystal structure of the catalytic domain of human MMP12 complexed with acetohydroxamic acid at atomic resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RMZpdb entry 1RMZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293Tris, PEG 6000, ACETOHYDROXAMIC ACID, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.242

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.913α = 90
b = 59.552β = 115.14
c = 53.497γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHdouble-crystal, Si(111) and Si(220)2004-07-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2R0.99993ELETTRA5.2R

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
11.0248.497.60.0570.0575.53.770833708336.63
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)RedundancyNumber Unique Reflections (All)
11.021.0884.90.2510.2512.73.18671

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 1RMZ1.0313.99652836528355171000.15660.15660.155630.16787RANDOM8.688
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]
0.04-0.120.09-0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.082
r_dihedral_angle_4_deg14.416
r_dihedral_angle_3_deg11.832
r_dihedral_angle_1_deg6.382
r_sphericity_free3.907
r_scangle_it3.254
r_sphericity_bonded2.65
r_scbond_it2.21
r_mcangle_it1.635
r_angle_refined_deg1.379
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.082
r_dihedral_angle_4_deg14.416
r_dihedral_angle_3_deg11.832
r_dihedral_angle_1_deg6.382
r_sphericity_free3.907
r_scangle_it3.254
r_sphericity_bonded2.65
r_scbond_it2.21
r_mcangle_it1.635
r_angle_refined_deg1.379
r_mcbond_it1.125
r_rigid_bond_restr1.104
r_angle_other_deg0.721
r_mcbond_other0.523
r_nbd_refined0.216
r_nbtor_refined0.2
r_symmetry_vdw_other0.199
r_nbd_other0.185
r_symmetry_vdw_refined0.183
r_symmetry_hbond_refined0.146
r_xyhbond_nbd_refined0.129
r_metal_ion_refined0.11
r_nbtor_other0.09
r_chiral_restr0.075
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.004
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1238
Nucleic Acid Atoms
Solvent Atoms287
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing