2OY2

Human MMP-8 in complex with peptide IAG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BZSpdb entry 1BZS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP82980.1M Tris-HCl, 20% PEG3350, 200mM acetohydroxamic acid, 0.2M MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3848.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.207α = 90
b = 68.533β = 98.1
c = 78.281γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHFixed exit double crystal Si [111], horizontally focussing2006-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7AEMBL/DESY, HAMBURGBW7A

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
11.538.751000.0820.0826.66.7556075560710.2
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)RedundancyNumber Unique Reflections (All)
1.51.581000.3140.3142.268108

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 1BZS1.538.75505075050750981000.16640.16640.163750.19237RANDOM12.388
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]
-0.14-0.05-0.350.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.625
r_dihedral_angle_4_deg16.734
r_dihedral_angle_3_deg12.546
r_dihedral_angle_1_deg5.785
r_scangle_it2.815
r_sphericity_free2.587
r_scbond_it2.291
r_rigid_bond_restr2.179
r_sphericity_bonded1.716
r_mcangle_it1.275
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.625
r_dihedral_angle_4_deg16.734
r_dihedral_angle_3_deg12.546
r_dihedral_angle_1_deg5.785
r_scangle_it2.815
r_sphericity_free2.587
r_scbond_it2.291
r_rigid_bond_restr2.179
r_sphericity_bonded1.716
r_mcangle_it1.275
r_angle_refined_deg1.119
r_mcbond_it0.762
r_nbtor_refined0.303
r_symmetry_vdw_refined0.255
r_nbd_refined0.193
r_xyhbond_nbd_refined0.128
r_symmetry_hbond_refined0.115
r_metal_ion_refined0.088
r_chiral_restr0.081
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 AtomsNumber
Protein Atoms2516
Nucleic Acid Atoms
Solvent Atoms565
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing