3RST

Crystal structure of Bacillus subtilis signal peptide peptidase A


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5291.15100mM Tris pH 8.5 23% Tert-butanol 5% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Crystal Properties
Matthews coefficientSolvent content
2.6754.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.779α = 90
b = 131.066β = 90
c = 207.263γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-300vertical collimating mirror2011-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

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
12.375099.80.08552.77.496535965352-3
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)
12.372.4999.80.2947.86.9

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 REPLACEMENTTHROUGHOUT3BFO , Chain A, C-terminal Domain (residues 326-549)2.37509599891450480698.160.207480.205710.24052RANDOM48.998
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]
-0.341.1-0.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.545
r_dihedral_angle_3_deg16.322
r_dihedral_angle_4_deg13.573
r_dihedral_angle_1_deg5.31
r_scangle_it2.736
r_scbond_it1.648
r_angle_refined_deg1.135
r_mcangle_it0.888
r_mcbond_it0.443
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.545
r_dihedral_angle_3_deg16.322
r_dihedral_angle_4_deg13.573
r_dihedral_angle_1_deg5.31
r_scangle_it2.736
r_scbond_it1.648
r_angle_refined_deg1.135
r_mcangle_it0.888
r_mcbond_it0.443
r_chiral_restr0.074
r_bond_refined_d0.01
r_gen_planes_refined0.005
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13685
Nucleic Acid Atoms
Solvent Atoms257
Heterogen Atoms

Software

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