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STRUCTURE of UNCLEAVED GLYCINE-BOUND HUMAN L-ASPARAGINASE PROTEIN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GDT PDB ENTRY 4GDT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 293 2.2 M SODIUM MALONATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.42 49.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.94 α = 90 b = 59.94 β = 90 c = 301.1 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD MARMOSAIC 300 mm CCD 2012-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.95 51.91 94.7 43500
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 1.95 2 90
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 4GDT 1.95 29.39 41251 41251 2248 98 0.169 0.167 0.1678 0.209 0.2115 RANDOM 24.2
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] -4.24 -4.24 8.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.962 r_dihedral_angle_4_deg 18.498 r_dihedral_angle_3_deg 18.05 r_dihedral_angle_1_deg 6.43 r_scangle_it 2.171 r_scbond_it 1.464 r_angle_refined_deg 1.354 r_mcangle_it 0.944 r_mcbond_it 0.533 r_chiral_restr 0.092
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.962 r_dihedral_angle_4_deg 18.498 r_dihedral_angle_3_deg 18.05 r_dihedral_angle_1_deg 6.43 r_scangle_it 2.171 r_scbond_it 1.464 r_angle_refined_deg 1.354 r_mcangle_it 0.944 r_mcbond_it 0.533 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4362 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 27
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement XDS data reduction XDS data scaling