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The structure of KdgF from Yersinia enterocolitica with malonate bound in the active site.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FPX PDB ENTRY 5FPX
Crystallization Crystal Properties Matthews coefficient Solvent content 2.84 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.19 α = 90 b = 60.19 β = 90 c = 67.831 γ = 120
Symmetry Space Group P 32 2 1
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 53 99.8 0.06 13.3 4.9 23188 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 1.54 100 0.4 2.7 4
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 5FPX 1.5 52.13 21989 1185 99.72 0.17139 0.16975 0.1725 0.20488 0.1978 RANDOM 18.722
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] -0.07 -0.03 -0.07 0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.723 r_dihedral_angle_4_deg 23.16 r_dihedral_angle_3_deg 10.044 r_dihedral_angle_1_deg 7.271 r_scbond_it 1.926 r_mcangle_it 1.788 r_angle_refined_deg 1.417 r_mcbond_it 1.102 r_mcbond_other 1.085 r_angle_other_deg 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.723 r_dihedral_angle_4_deg 23.16 r_dihedral_angle_3_deg 10.044 r_dihedral_angle_1_deg 7.271 r_scbond_it 1.926 r_mcangle_it 1.788 r_angle_refined_deg 1.417 r_mcbond_it 1.102 r_mcbond_other 1.085 r_angle_other_deg 0.75 r_chiral_restr 0.092 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 876 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement PHASER phasing