2BWU

Asp271Ala Escherichia coli Aminopeptidase P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BHCPDB ENTRY 2BHC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5277SITTING DROP VAPOUR DIFFUSION AT 4C. 2 UL 10 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 30% MPD, 0.1 M CITRATE PH 7.5, 0.2 M MGACETATE. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH AND 1 MM MNCL2 FOR 1 HR AT 4C PRIOR TO CRYOCOOLING.
Crystal Properties
Matthews coefficientSolvent content
5.677.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.589α = 90
b = 138.589β = 90
c = 232.056γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2005-05-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-2SSRLBL9-2

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
12.222.5899.40.0613.64.156922650.46
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)
12.22.321000.551.84.1

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 2BHC2.222.6553699279998.60.1710.170.193RANDOM57.52
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]
2.012.01-4.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.514
r_dihedral_angle_4_deg16.203
r_dihedral_angle_3_deg12.436
r_dihedral_angle_1_deg5.827
r_scangle_it4.44
r_scbond_it2.518
r_mcangle_it1.577
r_angle_refined_deg1.181
r_angle_other_deg0.765
r_mcbond_it0.765
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.514
r_dihedral_angle_4_deg16.203
r_dihedral_angle_3_deg12.436
r_dihedral_angle_1_deg5.827
r_scangle_it4.44
r_scbond_it2.518
r_mcangle_it1.577
r_angle_refined_deg1.181
r_angle_other_deg0.765
r_mcbond_it0.765
r_symmetry_vdw_refined0.299
r_symmetry_vdw_other0.258
r_nbd_refined0.198
r_nbtor_refined0.172
r_nbd_other0.169
r_xyhbond_nbd_refined0.129
r_symmetry_hbond_refined0.094
r_nbtor_other0.08
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3484
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALEPACKdata scaling