3DLJ | pdb_00003dlj

Crystal structure of human carnosine dipeptidase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZOFPDB entry 2ZOF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529730% PEG 4000, 0.2M Ammonium sulfate, 0.1M Na Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties
Matthews coefficientSolvent content
2.6253.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.106α = 90
b = 75.613β = 109.79
c = 103.716γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDAdjustable focus K-B pair Si plus Pt, Rh coatings2008-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.96749APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.255097.40.0610.06111.63.6514185141842.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.3385.40.4010.4012.32.8

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2ZOF2.2629.915025550255105197.290.201090.200020.240.254020.28RANDOM35.634
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]
0.220.09-0.280.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.676
r_dihedral_angle_4_deg21.255
r_dihedral_angle_3_deg14.691
r_dihedral_angle_1_deg6.451
r_scangle_it2.684
r_scbond_it1.727
r_angle_refined_deg1.364
r_mcangle_it1.092
r_mcbond_it0.648
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.676
r_dihedral_angle_4_deg21.255
r_dihedral_angle_3_deg14.691
r_dihedral_angle_1_deg6.451
r_scangle_it2.684
r_scbond_it1.727
r_angle_refined_deg1.364
r_mcangle_it1.092
r_mcbond_it0.648
r_nbtor_refined0.305
r_symmetry_vdw_refined0.222
r_nbd_refined0.194
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.101
r_metal_ion_refined0.1
r_chiral_restr0.09
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7183
Nucleic Acid Atoms
Solvent Atoms213
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
ARP/wARPmodel building