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PLP-dependent phospholyase A1RDF1 from Arthrobacter aurescens TC1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 24% (W/V) PEG 3350, 0.2 M (NH4)2SO4 AND 3% (V/V) 2-METHYL-2,4-PENTANEDIOL IN 0.1 M BIS-TRIS PROPANE BUFFER AT PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.42 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.937 α = 90 b = 97.176 β = 90 c = 124.261 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 120 PIXEL DECTRIS PILATUS 2M 2015-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.5 76.55 99.8 0.06 21.6 8.2 148178 2
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 1.5 1.53 98.8 0.53 4.1 8.5
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 NONE 1.5 76.55 140870 7218 99.27 0.1543 0.15321 0.1662 0.17549 0.1864 RANDOM 17.456
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] -0.99 -0.78 1.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.799 r_dihedral_angle_4_deg 16.633 r_dihedral_angle_3_deg 12.25 r_dihedral_angle_1_deg 6.07 r_scbond_it 2.97 r_mcangle_it 2.256 r_angle_refined_deg 2.251 r_angle_other_deg 1.714 r_mcbond_it 1.657 r_mcbond_other 1.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.799 r_dihedral_angle_4_deg 16.633 r_dihedral_angle_3_deg 12.25 r_dihedral_angle_1_deg 6.07 r_scbond_it 2.97 r_mcangle_it 2.256 r_angle_refined_deg 2.251 r_angle_other_deg 1.714 r_mcbond_it 1.657 r_mcbond_other 1.625 r_chiral_restr 0.136 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 r_bond_other_d 0.01 r_gen_planes_other 0.007 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_mcangle_other r_scbond_other r_scangle_it 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 6331 Nucleic Acid Atoms Solvent Atoms 665 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling BALBES phasing