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The structure of KdgF from Yersinia enterocolitica.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PFW PDB ENTRY 2PFW
Crystallization Crystal Properties Matthews coefficient Solvent content 2.24 45.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.92 α = 90 b = 73.76 β = 90 c = 83.68 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 113 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-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 30 97.3 0.03 32.2 7.2 39140 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 78.5 0.44 3.6 6.1
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 2PFW 1.5 55.33 37178 1962 96.95 0.17264 0.17118 0.1816 0.19928 0.2033 RANDOM 23.368
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] 2.44 -0.84 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.601 r_dihedral_angle_4_deg 24.339 r_dihedral_angle_3_deg 12.593 r_dihedral_angle_1_deg 8.299 r_mcangle_it 3.345 r_scbond_it 2.665 r_mcbond_it 2.112 r_mcbond_other 2.108 r_angle_refined_deg 1.827 r_angle_other_deg 0.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.601 r_dihedral_angle_4_deg 24.339 r_dihedral_angle_3_deg 12.593 r_dihedral_angle_1_deg 8.299 r_mcangle_it 3.345 r_scbond_it 2.665 r_mcbond_it 2.112 r_mcbond_other 2.108 r_angle_refined_deg 1.827 r_angle_other_deg 0.863 r_chiral_restr 0.104 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.002 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_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 1788 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing