X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNative aminopeptidase P without water, Mn or multiple conformers

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.3298TRIS, PEG 4000, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
4.472

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.322α = 90
b = 177.322β = 90
c = 96.312γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IICYALE MIRRORS1998-08-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200H1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.15090.232.934722147221-3
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)
12.12.1859.40.07172200

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTNative aminopeptidase P without water, Mn or multiple conformers2.1504574645746147590.260.150360.149390.17997RANDOM18.815
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]
-0.18-0.09-0.180.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.695
r_dihedral_angle_4_deg14.914
r_dihedral_angle_3_deg12.137
r_dihedral_angle_1_deg6.09
r_scangle_it3.884
r_mcangle_it2.752
r_scbond_it2.651
r_mcbond_it2.365
r_angle_refined_deg1.29
r_angle_other_deg0.795
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.695
r_dihedral_angle_4_deg14.914
r_dihedral_angle_3_deg12.137
r_dihedral_angle_1_deg6.09
r_scangle_it3.884
r_mcangle_it2.752
r_scbond_it2.651
r_mcbond_it2.365
r_angle_refined_deg1.29
r_angle_other_deg0.795
r_mcbond_other0.568
r_symmetry_vdw_other0.311
r_symmetry_vdw_refined0.227
r_nbd_refined0.204
r_nbd_other0.181
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.15
r_symmetry_hbond_refined0.143
r_nbtor_other0.081
r_chiral_restr0.075
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3499
Nucleic Acid Atoms
Solvent Atoms456
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling