4AR1

Crystal Structure of the Peptidase Domain of Collagenase H from Clostridium histolyticum at 2.01 Angstrom resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Y3UPDB ENTRY 2Y3U

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.2522.5% PEG3350 AND 0.15M SODIUM FORMATE, PH 7.25
Crystal Properties
Matthews coefficientSolvent content
2.4750.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.05α = 90
b = 108.23β = 90
c = 51.27γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.0146.3399.80.147.85.829831223.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.012.1299.60.7625.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2Y3U2.0146.3328276151199.650.202720.200280.24953RANDOM26.759
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]
0.781.55-2.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.139
r_sphericity_free20.475
r_dihedral_angle_4_deg19.851
r_dihedral_angle_3_deg15.206
r_sphericity_bonded8.327
r_dihedral_angle_1_deg5.661
r_rigid_bond_restr4.546
r_angle_refined_deg0.988
r_angle_other_deg0.829
r_chiral_restr0.059
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.139
r_sphericity_free20.475
r_dihedral_angle_4_deg19.851
r_dihedral_angle_3_deg15.206
r_sphericity_bonded8.327
r_dihedral_angle_1_deg5.661
r_rigid_bond_restr4.546
r_angle_refined_deg0.988
r_angle_other_deg0.829
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.003
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3106
Nucleic Acid Atoms
Solvent Atoms168
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing