☰ Navigation Tabs
Crystal structure of a putative d-serine deaminase (bxe_a4060) from burkholderia xenovorans lb400 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 1.0000M NaCitrate, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.46 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.637 α = 90 b = 113.637 β = 90 c = 145.92 γ = 90
Symmetry Space Group P 41 21 2
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 MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2009-01-08 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97925 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 29.881 99 0.109 0.109 11.1 4.9 64237 25.981
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 100 0.695 0.695 1.8 4.9 4742
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2 29.881 64159 3250 98.62 0.165 0.163 0.1689 0.205 0.2087 RANDOM 30.499
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] -0.46 -0.46 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.918 r_dihedral_angle_4_deg 20.801 r_dihedral_angle_3_deg 13.236 r_scangle_it 6.846 r_dihedral_angle_1_deg 5.983 r_scbond_it 4.83 r_mcangle_it 2.74 r_mcbond_it 1.669 r_angle_refined_deg 1.438 r_angle_other_deg 0.956
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.918 r_dihedral_angle_4_deg 20.801 r_dihedral_angle_3_deg 13.236 r_scangle_it 6.846 r_dihedral_angle_1_deg 5.983 r_scbond_it 4.83 r_mcangle_it 2.74 r_mcbond_it 1.669 r_angle_refined_deg 1.438 r_angle_other_deg 0.956 r_mcbond_other 0.739 r_symmetry_vdw_other 0.27 r_symmetry_vdw_refined 0.228 r_nbd_other 0.205 r_nbd_refined 0.201 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.086 r_nbtor_other 0.085 r_metal_ion_refined 0.068 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6218 Nucleic Acid Atoms Solvent Atoms 471 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing