3FH4

Crystal Structure of Recombinant Vibrio proteolyticus aminopeptidase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293VpAP (0.5 mM) in 10 mM Tris buffer, pH 8.0, containing 10 mM KSCN and 400 mM NaCl was equilibrated with 100 mM Tris buffer, pH 8.0, containing 100 mM KSCN and 4.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4650.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 108.397α = 90
b = 108.397β = 90
c = 93.529γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray98IMAGE PLATERIGAKU RAXIS IV++mirrors2008-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.9541.891000.13521231582
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.951000.51531.521

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2IQ61.9526.031701321990116895.710.192940.191150.22776RANDOM15.414
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.533
r_dihedral_angle_4_deg15.244
r_dihedral_angle_3_deg12.788
r_dihedral_angle_1_deg5.56
r_scangle_it2.038
r_scbond_it1.279
r_angle_refined_deg1.083
r_mcangle_it0.855
r_mcbond_it0.454
r_nbtor_refined0.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.533
r_dihedral_angle_4_deg15.244
r_dihedral_angle_3_deg12.788
r_dihedral_angle_1_deg5.56
r_scangle_it2.038
r_scbond_it1.279
r_angle_refined_deg1.083
r_mcangle_it0.855
r_mcbond_it0.454
r_nbtor_refined0.297
r_symmetry_vdw_refined0.202
r_symmetry_hbond_refined0.197
r_nbd_refined0.192
r_xyhbond_nbd_refined0.124
r_metal_ion_refined0.081
r_chiral_restr0.073
r_bond_refined_d0.009
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_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 Atoms2235
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms12

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling