X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherNATIVE AMINOPEPTIDASE P WITHOUT HETATOMS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPTRIS, PEG 4000, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
4.472

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.733α = 90
b = 177.733β = 90
c = 96.484γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113IMAGE PLATERIGAKU RAXIS IICYALE MIRRORS1998-08-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
1242.2692.426.535617456174-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0564.25.39

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 HETATOMS242.265446454464170892.440.148320.147510.17336RANDOM17.504
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]
-0.13-0.06-0.130.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.765
r_dihedral_angle_4_deg15.015
r_dihedral_angle_3_deg12.207
r_dihedral_angle_1_deg6.003
r_scangle_it3.878
r_mcangle_it2.695
r_scbond_it2.53
r_mcbond_it2.371
r_angle_refined_deg1.296
r_angle_other_deg0.797
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.765
r_dihedral_angle_4_deg15.015
r_dihedral_angle_3_deg12.207
r_dihedral_angle_1_deg6.003
r_scangle_it3.878
r_mcangle_it2.695
r_scbond_it2.53
r_mcbond_it2.371
r_angle_refined_deg1.296
r_angle_other_deg0.797
r_mcbond_other0.57
r_symmetry_vdw_other0.283
r_symmetry_vdw_refined0.282
r_nbd_refined0.207
r_nbd_other0.181
r_nbtor_refined0.176
r_symmetry_hbond_refined0.16
r_xyhbond_nbd_refined0.145
r_nbtor_other0.081
r_chiral_restr0.074
r_bond_refined_d0.011
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3499
Nucleic Acid Atoms
Solvent Atoms599
Heterogen Atoms43

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling