3QJX

Crystal Structure of E. coli Aminopeptidase N in complex with L-Serine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52981.8M Sodium Malonate, L-serine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.5164.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.23α = 90
b = 120.23β = 90
c = 170.801γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-05-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.21.0000ALS8.2.2

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
11.4535.7499.90.06213.95.425119024403511
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)
11.451.5399.80.5372.85.536315

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.4535.74244035764199.910.121080.120270.14709RANDOM15.237
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]
0.020.010.02-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.82
r_dihedral_angle_4_deg20.081
r_dihedral_angle_3_deg13.09
r_scangle_it8.322
r_dihedral_angle_1_deg6.03
r_scbond_it5.849
r_mcangle_it3.788
r_rigid_bond_restr3.306
r_mcbond_it2.695
r_angle_refined_deg2.601
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.82
r_dihedral_angle_4_deg20.081
r_dihedral_angle_3_deg13.09
r_scangle_it8.322
r_dihedral_angle_1_deg6.03
r_scbond_it5.849
r_mcangle_it3.788
r_rigid_bond_restr3.306
r_mcbond_it2.695
r_angle_refined_deg2.601
r_chiral_restr0.193
r_bond_refined_d0.032
r_gen_planes_refined0.015
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6940
Nucleic Acid Atoms
Solvent Atoms922
Heterogen Atoms96

Software

Software
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling