4HXE

Pyrococcus horikoshii acylaminoacyl peptidase (uncomplexed)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52983.0 M 1,6-hexanediol, 0.20 M MgCl2, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1861.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183α = 90
b = 183β = 90
c = 144.63γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IIC2005-06-17MSINGLE WAVELENGTH
21x-ray100IMAGE PLATERIGAKU RAXIS IIC2006-03-23MSINGLE WAVELENGTH
31x-ray100IMAGE PLATERIGAKU RAXIS IIC2006-03-03MSINGLE WAVELENGTH
41x-ray100CCDMAR CCD 165 mmmirrors2006-06-29MMAD
51x-ray100CCDMARMOSAIC 225 mm CCDmirrors2006-06-29MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418
2ROTATING ANODERIGAKU RU2001.5418
3ROTATING ANODERIGAKU RU2001.5418
4SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8162EMBL/DESY, HAMBURGX11
5SYNCHROTRONESRF BEAMLINE BM141.0715ESRFBM14

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
1,2,3,41.92095.70.15812.798.326973869738-320.794
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)
1,2,3,41.9274.60.6861.872.847680

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMIRASTHROUGHOUT1.9119.786480164801342595.160.17410.17410.172190.21021RANDOM21.562
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_deg36.397
r_dihedral_angle_4_deg19.616
r_dihedral_angle_3_deg15.731
r_dihedral_angle_1_deg7.388
r_angle_refined_deg1.944
r_chiral_restr0.155
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.397
r_dihedral_angle_4_deg19.616
r_dihedral_angle_3_deg15.731
r_dihedral_angle_1_deg7.388
r_angle_refined_deg1.944
r_chiral_restr0.155
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4959
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms51

Software

Software
Software NamePurpose
bioteXdata collection
SHELXmodel building
MLPHAREphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing