☰ Navigation Tabs
D-xylose Isomerase in complex with linear product, per-deuterated xylulose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XIS PDB entry 4XIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 293 50MM TRIS-HCL, 38%(NH4)2SO4, 2MM MG2+ XI @ 125 MG/ML, PH=8.0, LIQUID DIFFUSION, T=293K; NATIVE CRYSTAL WERE SOAKED WITH 0.2M PER-DEUTERATED XYLOSE IN D2O BUFFERED IN 50MM TRIS-DCL, PH=7.6 (PD=8.0), 2MM MGCL2
Crystal Properties Matthews coefficient Solvent content 2.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.64 α = 90 b = 99.97 β = 90 c = 103.97 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 neutron 293 AREA DETECTOR TIME-OF-FLIGHT MULTIWIRE HE3 NE 2004-09-01 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR PCS
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.2 100 89.4 0.25 5.8 5.4 21892 1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 81.3 0.38 2 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B NEUTRON DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB entry 4XIS 2.2 20 17072 876 86.3 0.237 0.288 RANDOM 20.7
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]
RMS Deviations Key Refinement Restraint Deviation s_angle_d 0.962 s_bond_d 0.007 s_similar_dist s_from_restr_planes s_zero_chiral_vol s_non_zero_chiral_vol s_anti_bump_dis_restr s_rigid_bond_adp_cmpnt s_similar_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3046 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 13
Software Software Software Name Purpose CNS refinement SHELXL-97 refinement d*TREK data reduction LAUENORM data scaling CNS phasing