☰ Navigation Tabs
Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IPP beta-S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3K4O PDB Entry 3K4O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 1.6M ammonium sulfate, 5mM ATP gamma-S, 1mM
IP, 2mM magnesium chloride., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.85 56.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.68 α = 90 b = 100.24 β = 90 c = 87.79 γ = 90
Symmetry Space Group P 21 21 2
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 2008-08-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 1.0 ALS 8.2.2
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 2.34 50 99 0.07 14.65 7.01 29535 29290 -3 57.911
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) 2.34 2.44 91.7 0.583 3 6.76 4681
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 3K4O 2.34 42.11 29289 1468 99.45 0.222 0.22 0.221 0.259 0.226 RANDOM 51.764
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] 0.78 1.59 -2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.819 r_dihedral_angle_3_deg 18.499 r_dihedral_angle_4_deg 16.276 r_dihedral_angle_1_deg 6.817 r_scangle_it 4.63 r_scbond_it 2.896 r_mcangle_it 2.108 r_angle_refined_deg 1.985 r_mcbond_it 1.16 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.819 r_dihedral_angle_3_deg 18.499 r_dihedral_angle_4_deg 16.276 r_dihedral_angle_1_deg 6.817 r_scangle_it 4.63 r_scbond_it 2.896 r_mcangle_it 2.108 r_angle_refined_deg 1.985 r_mcbond_it 1.16 r_chiral_restr 0.118 r_bond_refined_d 0.02 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4075 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 48
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction MOLREP phasing