☰ Navigation Tabs
Structure of L-Amino acid deaminase from Proteus myxofaciens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GAG PDB ENTRY 2GAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 15% PEG 6K, 0.1 M MES (PH 6.5), 10% MPD
Crystal Properties Matthews coefficient Solvent content 2.48 50.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.76 α = 90 b = 93.71 β = 102.85 c = 74.69 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 ADSC CCD 2015-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2 49.08 99.9 0.09 12 4.5 65982 3
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 2 2.11 99.9 0.51 2.9 4.7
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 2GAG 2 46.85 62619 3340 99.9 0.17855 0.17691 0.1844 0.20898 0.2129 RANDOM 25.967
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] -0.03 -0.04 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.195 r_dihedral_angle_4_deg 14.369 r_dihedral_angle_3_deg 13.034 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 3.805 r_long_range_B_other 3.712 r_scangle_other 1.764 r_mcangle_it 1.754 r_mcangle_other 1.754 r_angle_refined_deg 1.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.195 r_dihedral_angle_4_deg 14.369 r_dihedral_angle_3_deg 13.034 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 3.805 r_long_range_B_other 3.712 r_scangle_other 1.764 r_mcangle_it 1.754 r_mcangle_other 1.754 r_angle_refined_deg 1.137 r_scbond_it 1.016 r_scbond_other 1.016 r_mcbond_it 1.001 r_mcbond_other 1.001 r_angle_other_deg 0.73 r_chiral_restr 0.062 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 6888 Nucleic Acid Atoms Solvent Atoms 517 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing