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Crystal structure of circularly permuted human asparaginase-like protein 1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 297 24 % PEG4000, 4 mM DTT, 0.15 mM Sodium citrate, pH4.6
Microseeding
Crystal Properties Matthews coefficient Solvent content 2.63 53.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.308 α = 90 b = 111.107 β = 90 c = 122.517 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 315r 2014-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.98 ALS 5.0.3
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 2.35 50 99.6 0.151 10.38 5.1 49346
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.35 2.39 99.9 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 THROUGHOUT 2.51 39.74 46618 2485 99.48 0.20569 0.20419 0.2091 0.23331 0.2378 RANDOM 28.501
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] 2.25 -1.15 -1.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.1 r_dihedral_angle_4_deg 18.093 r_dihedral_angle_3_deg 14.78 r_long_range_B_refined 6.946 r_long_range_B_other 6.945 r_dihedral_angle_1_deg 6.568 r_scangle_other 4.985 r_mcangle_it 3.636 r_mcangle_other 3.636 r_scbond_it 3.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.1 r_dihedral_angle_4_deg 18.093 r_dihedral_angle_3_deg 14.78 r_long_range_B_refined 6.946 r_long_range_B_other 6.945 r_dihedral_angle_1_deg 6.568 r_scangle_other 4.985 r_mcangle_it 3.636 r_mcangle_other 3.636 r_scbond_it 3.184 r_scbond_other 3.18 r_mcbond_other 2.32 r_mcbond_it 2.318 r_angle_refined_deg 1.684 r_angle_other_deg 1.175 r_chiral_restr 0.088 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.007 r_gen_planes_other 0.005 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 Atoms Number Protein Atoms 8584 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing