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Crystal structure of PfkB protein from Polaromonas sp. JS666
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1V19 pdb entry 1V19
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2M NaCl, 0.1M Bis-tris, 25% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.923 α = 90 b = 83.084 β = 90 c = 196.202 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 100 CCD ADSC QUANTUM 315 Mirrors 2012-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9791 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 2.51 50 98.2 0.08 7.8 12.9 46596 46596
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 2.51 2.6 92.6 0.47 4 12.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1V19 2.7 43.68 46596 35792 1890 98.87 0.22939 0.22581 0.2252 0.29649 0.2924 RANDOM 31.832
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] 0.08 0.02 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.709 r_dihedral_angle_3_deg 22.483 r_dihedral_angle_4_deg 20.099 r_dihedral_angle_1_deg 7.159 r_scangle_it 3.882 r_scbond_it 2.498 r_angle_refined_deg 1.689 r_mcangle_it 1.443 r_mcbond_it 0.753 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.709 r_dihedral_angle_3_deg 22.483 r_dihedral_angle_4_deg 20.099 r_dihedral_angle_1_deg 7.159 r_scangle_it 3.882 r_scbond_it 2.498 r_angle_refined_deg 1.689 r_mcangle_it 1.443 r_mcbond_it 0.753 r_chiral_restr 0.109 r_bond_refined_d 0.015 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8526 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 2
Software Software Software Name Purpose CBASS data collection MOLREP phasing Coot model building ARP model building AutoSol phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling