2H1N

3.0 A X-ray structure of putative oligoendopeptidase F: crystals grown by vapor diffusion technique


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7298Hampton research SaltRX condition #96: 0.1M Bis-Tris Propane buffer, 60% Tascimate, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
3.8768.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.987α = 90
b = 119.987β = 90
c = 249.747γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDADJUSTABLE FOCUSING MIRRORS. K-B GEOMETRY2006-04-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-DAPS23-ID-D

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
135098.70.04717.65.642052
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)
133.1198.30.362.15.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT3204158139493208898.20.1860.1850.211RANDOM63.66
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]
0.670.340.67-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.909
r_dihedral_angle_3_deg19.001
r_dihedral_angle_4_deg17.374
r_dihedral_angle_1_deg4.871
r_scangle_it1.857
r_scbond_it1.238
r_angle_refined_deg1.047
r_mcangle_it0.733
r_mcbond_it0.537
r_nbtor_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.909
r_dihedral_angle_3_deg19.001
r_dihedral_angle_4_deg17.374
r_dihedral_angle_1_deg4.871
r_scangle_it1.857
r_scbond_it1.238
r_angle_refined_deg1.047
r_mcangle_it0.733
r_mcbond_it0.537
r_nbtor_refined0.322
r_nbd_refined0.225
r_symmetry_vdw_refined0.192
r_symmetry_hbond_refined0.185
r_xyhbond_nbd_refined0.123
r_chiral_restr0.075
r_bond_refined_d0.01
r_gen_planes_refined0.003
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_refined
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9358
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms14

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing