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Crystal structure of apo xylose isomerase from Piromyces E2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NH5 D_1200004044
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 294 13-15 % PEG3350, Hepes buffer pH 7
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.931 α = 115.77 b = 79.286 β = 89.5 c = 91.106 γ = 116.73
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH 2014-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) 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 1.67 59 93.3 0.078 0.054 0.995 9.1 4 187268
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.7 88.9 0.286 0.206 0.84 3.7 3.8
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 D_1200004044 1.67 59 177867 9338 93.3 0.18504 0.18372 0.191 0.21005 0.2175 RANDOM 14.024
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 0.01 -0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.496 r_dihedral_angle_4_deg 13.931 r_dihedral_angle_3_deg 12.569 r_dihedral_angle_1_deg 5.695 r_long_range_B_refined 4.812 r_long_range_B_other 4.811 r_angle_refined_deg 1.312 r_scangle_other 1.203 r_angle_other_deg 0.937 r_mcangle_it 0.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.496 r_dihedral_angle_4_deg 13.931 r_dihedral_angle_3_deg 12.569 r_dihedral_angle_1_deg 5.695 r_long_range_B_refined 4.812 r_long_range_B_other 4.811 r_angle_refined_deg 1.312 r_scangle_other 1.203 r_angle_other_deg 0.937 r_mcangle_it 0.789 r_mcangle_other 0.789 r_scbond_it 0.768 r_scbond_other 0.768 r_mcbond_it 0.463 r_mcbond_other 0.461 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 13866 Nucleic Acid Atoms Solvent Atoms 2317 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing