☰ Navigation Tabs
A case study for twinned data analysis: multiple crystal forms of the enzyme N-acetyl-neuraminic lyase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XFW PDB ENTRY 2XFW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.2 100MM TRIS-HCL PH 8.2, 200MM NACL, 18% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.58 52.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.985 α = 90 b = 116.665 β = 118.06 c = 83.678 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC CCD 2008-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 1.8 73.92 100 0.12 1 7.2 122053 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 1.8 1.9 100 0.53 4.9 7.3
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 PDB ENTRY 2XFW 1.79 73.85 115868 6147 98.44 0.15683 0.15539 0.189 0.18383 0.2174 RANDOM 12.828
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] 5.61 -0.76 7.27 -12.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.321 r_dihedral_angle_4_deg 19.319 r_dihedral_angle_3_deg 11.917 r_dihedral_angle_1_deg 5.494 r_angle_refined_deg 1.134 r_angle_other_deg 0.854 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.321 r_dihedral_angle_4_deg 19.319 r_dihedral_angle_3_deg 11.917 r_dihedral_angle_1_deg 5.494 r_angle_refined_deg 1.134 r_angle_other_deg 0.854 r_chiral_restr 0.066 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it 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 9270 Nucleic Acid Atoms Solvent Atoms 745 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement