4P10

pro-carboxypeptidase U In Complex With 5-(3-aminopropyl)-1-propyl-6,7-dihydro-4H-benzimidazole-5-carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZG7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293Crystallisation was done using the hanging drop method equilibrating over a well solution containing 10% (w/v) PEG20k, 2% dioxane and 0.1M bicine pH 9.0. Crystals were then soaked in well solution supplemented with 1 mM compound
Crystal Properties
Matthews coefficientSolvent content
2.5150.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.576α = 90
b = 49.243β = 93.12
c = 95.048γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 12007-01-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.954ESRFID23-1

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
124099.17.14.130908
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)
122.0598.50.3092.74.2

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 REPLACEMENTTHROUGHOUT1ZG7294.9129202154798.680.185720.183980.21812RANDOM27.115
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]
-1.660.513.79-2.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.92
r_dihedral_angle_4_deg17.583
r_dihedral_angle_3_deg14.168
r_dihedral_angle_1_deg7.419
r_long_range_B_refined4.927
r_long_range_B_other4.865
r_scangle_other3.79
r_mcangle_it2.925
r_mcangle_other2.924
r_scbond_it2.677
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.92
r_dihedral_angle_4_deg17.583
r_dihedral_angle_3_deg14.168
r_dihedral_angle_1_deg7.419
r_long_range_B_refined4.927
r_long_range_B_other4.865
r_scangle_other3.79
r_mcangle_it2.925
r_mcangle_other2.924
r_scbond_it2.677
r_scbond_other2.677
r_mcbond_it2.133
r_mcbond_other2.131
r_angle_refined_deg1.741
r_angle_other_deg0.92
r_chiral_restr0.119
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3254
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling