4QUO

Crystal structure of Aminopeptidase N in complex with the phosphinic dipeptide analogue LL-(R,S)-hPheP[CH2]Phe(3-CH2NH2)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GTQPDB ENTRY 2GTQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72912.0 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.8256.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 223.707α = 90
b = 223.707β = 90
c = 57.769γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2013-10-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.9794APS19-ID

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
11.654099.90.07183.712970012970022
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6899.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 DIFFRACTIONSADTHROUGHOUTPDB ENTRY 2GTQ1.6527.9822117723111770595390.610.150.149830.148130.18188RANDOM18.803
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]
0.160.160.16-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.639
r_dihedral_angle_4_deg18.178
r_dihedral_angle_3_deg13.145
r_dihedral_angle_1_deg6.003
r_angle_refined_deg2.035
r_angle_other_deg0.938
r_chiral_restr0.125
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.639
r_dihedral_angle_4_deg18.178
r_dihedral_angle_3_deg13.145
r_dihedral_angle_1_deg6.003
r_angle_refined_deg2.035
r_angle_other_deg0.938
r_chiral_restr0.125
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6847
Nucleic Acid Atoms
Solvent Atoms1041
Heterogen Atoms134

Software

Software
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
CCP4model building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing