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Crystal structure of human carnosine dipeptidase 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZOF PDB entry 2ZOF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 297 30% PEG 4000, 0.2M Ammonium sulfate, 0.1M Na Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.62 53.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.106 α = 90 b = 75.613 β = 109.79 c = 103.716 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD Adjustable focus K-B pair Si plus Pt, Rh coatings 2008-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.96749 APS 23-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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.25 50 97.4 0.061 0.061 11.6 3.6 51418 51418 42.7
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) Redundancy Number Unique Reflections (All) 1 2.25 2.33 85.4 0.401 0.401 2.3 2.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2ZOF 2.26 29.91 50255 50255 1051 97.29 0.20109 0.20002 0.2355 0.25402 0.2767 RANDOM 35.634
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] 0.22 0.09 -0.28 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.676 r_dihedral_angle_4_deg 21.255 r_dihedral_angle_3_deg 14.691 r_dihedral_angle_1_deg 6.451 r_scangle_it 2.684 r_scbond_it 1.727 r_angle_refined_deg 1.364 r_mcangle_it 1.092 r_mcbond_it 0.648 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.676 r_dihedral_angle_4_deg 21.255 r_dihedral_angle_3_deg 14.691 r_dihedral_angle_1_deg 6.451 r_scangle_it 2.684 r_scbond_it 1.727 r_angle_refined_deg 1.364 r_mcangle_it 1.092 r_mcbond_it 0.648 r_nbtor_refined 0.305 r_symmetry_vdw_refined 0.222 r_nbd_refined 0.194 r_xyhbond_nbd_refined 0.126 r_symmetry_hbond_refined 0.101 r_metal_ion_refined 0.1 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 7183 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling ARP/wARP model building