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PglD from Campylobacter jejuni NCTC 11168 in complex with 5-(2-furanyl)-1H-pyrazole-3-carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NPO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 295 pH 4.5, 0.1 mM sodium acetate, 1.9 M ammonium sulphate, 22 C
Crystal Properties Matthews coefficient Solvent content 3.33 63.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.726 α = 90 b = 86.726 β = 90 c = 65.53 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 2009-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.080900 NSLS X29A
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 2.1 50 97.9 0.061 24.3 2.1 16473
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 2.102 2.155 83.11 0.654 1.3
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 2NPO 2.1 12 15234 810 98.11 0.19823 0.196 0.195 0.2411 0.2408 RANDOM 45.668
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] 0.52 0.26 0.52 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.637 r_dihedral_angle_4_deg 21.832 r_dihedral_angle_3_deg 17.678 r_dihedral_angle_1_deg 6.129 r_scangle_it 5.424 r_scbond_it 3.188 r_mcangle_it 1.937 r_angle_refined_deg 1.699 r_mcbond_it 0.993 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.637 r_dihedral_angle_4_deg 21.832 r_dihedral_angle_3_deg 17.678 r_dihedral_angle_1_deg 6.129 r_scangle_it 5.424 r_scbond_it 3.188 r_mcangle_it 1.937 r_angle_refined_deg 1.699 r_mcbond_it 0.993 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_mcangle_other r_scbond_other 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 1384 Nucleic Acid Atoms Solvent Atoms 74 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MOLREP phasing SCALEPACK data scaling PHASER phasing HKL-2000 data reduction