☰ Navigation Tabs
L-amino acid deaminase from Proteus vulgaris
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 285 5% m/v PEG 20000, 200mM MES,1mM cetyltrimethylammonium bromide
Crystal Properties Matthews coefficient Solvent content 3.03 59.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.314 α = 64.52 b = 104.575 β = 73.06 c = 105.419 γ = 61.17
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 MAR CCD 165 mm 2006-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BSRF BEAMLINE 3W1A 1.000 BSRF 3W1A
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 2.63 94.63 97.2 31 3.8 97176
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 2.63 2.72
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 5I39 2.63 94.63 92242 4861 97.12 0.22282 0.22129 0.2211 0.25198 0.2516 RANDOM 91.747
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] -3.33 -1.28 1.69 1.94 0.51 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.251 r_dihedral_angle_3_deg 14.786 r_dihedral_angle_4_deg 10.741 r_dihedral_angle_1_deg 5.135 r_long_range_B_refined 3.513 r_angle_refined_deg 1.249 r_mcangle_it 1.043 r_scbond_it 0.589 r_mcbond_it 0.58 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.251 r_dihedral_angle_3_deg 14.786 r_dihedral_angle_4_deg 10.741 r_dihedral_angle_1_deg 5.135 r_long_range_B_refined 3.513 r_angle_refined_deg 1.249 r_mcangle_it 1.043 r_scbond_it 0.589 r_mcbond_it 0.58 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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_it r_scangle_other 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 19615 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms 618
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing