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L-asparaginase of E. coli in C2 space group and 1.95 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ECA PDB ENTRY 3ECA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 291 PEG 3350, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.14 42.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.296 α = 90 b = 134.617 β = 110.51 c = 64.867 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 IMAGE PLATE MARRESEARCH cyllindrical mirror and triangular bent single crystal monochromator. M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.38 LNLS D03B-MX1
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 1.95 13 91.8 0.047 1.55 40782
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 1.95 2 0.325 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3ECA 1.95 12.97 38737 2045 91.83 0.13176 0.12969 0.1317 0.17125 0.1727 RANDOM 18.58
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] 0.02 -0.01 -0.04 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.327 r_dihedral_angle_3_deg 17.165 r_dihedral_angle_4_deg 13.248 r_dihedral_angle_1_deg 5.796 r_scangle_it 5.536 r_scbond_it 3.328 r_angle_refined_deg 2.097 r_mcangle_it 1.87 r_mcbond_it 1.059 r_symmetry_hbond_refined 0.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.327 r_dihedral_angle_3_deg 17.165 r_dihedral_angle_4_deg 13.248 r_dihedral_angle_1_deg 5.796 r_scangle_it 5.536 r_scbond_it 3.328 r_angle_refined_deg 2.097 r_mcangle_it 1.87 r_mcbond_it 1.059 r_symmetry_hbond_refined 0.368 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.228 r_chiral_restr 0.203 r_xyhbond_nbd_refined 0.16 r_bond_refined_d 0.027 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_symmetry_vdw_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4862 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 18
Software Software Software Name Purpose MAR345 data collection SCALEPACK data scaling AMoRE phasing REFMAC refinement