☰ Navigation Tabs
Crystal structure of human Arginase-2 complexed with inhibitor 2d: {(5R)-5-amino-5-carboxy-5-[1-(4-chlorobenzyl)piperidin-4-yl]pentyl}(trihydroxy)borate(1-)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1D3V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 277 Crystals in condition H3 from Silver Bullet screen (Hampton Research) using Tacsimate in the reservoir, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.28 62.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.123 α = 90 b = 128.123 β = 90 c = 159.362 γ = 90
Symmetry Space Group P 42 21 2
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 RIGAKU SATURN 944 OSMIC MIRRORS 2009-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 33.83 92.8 0.128 11.3 5.4 54972 54972
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 97.6 0.355 3.6 4.4
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT R-free 1D3V 2.3 33.83 54957 54957 2774 92.38 0.1828 0.1828 0.1802 0.1821 0.2318 0.2327 Random 5% 17.6987
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.815 f_angle_d 1.43 f_chiral_restr 0.177 f_bond_d 0.01 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7010 Nucleic Acid Atoms Solvent Atoms 633 Heterogen Atoms 126
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling AMoRE phasing