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Crystal structure of Dipeptide Epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Val
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TKK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4 277 Precipitant contained 12% PEG 10000 and 0.1M Na-citrate, Protein solution contained 0.1M NaCl, 10% glycerol, and 0.02M D-Ala-L-Val. Protein concentration was 40 mg/mL, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.68 66.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94 α = 90 b = 158.2 β = 100.28 c = 182.74 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 RAYONIX MX-300 2010-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3 20 99.6 0.106 12.53 6.1 104809
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3 3.11 100 0.553 2.56
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1TKK 3 20 104811 99570 5241 100 0.274 0.22866 0.22749 0.25069 0.2484 RANDOM 70.323
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] -0.06 -0.11 0.2 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.441 r_dihedral_angle_4_deg 23.647 r_dihedral_angle_3_deg 17.341 r_scangle_it 11.381 r_scbond_it 8.538 r_mcangle_it 7.843 r_mcbond_it 5.792 r_dihedral_angle_1_deg 4.892 r_angle_refined_deg 1.026 r_chiral_restr 0.069
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.441 r_dihedral_angle_4_deg 23.647 r_dihedral_angle_3_deg 17.341 r_scangle_it 11.381 r_scbond_it 8.538 r_mcangle_it 7.843 r_mcbond_it 5.792 r_dihedral_angle_1_deg 4.892 r_angle_refined_deg 1.026 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25434 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 126
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling