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Crystal Structure of Isopentenyl Phosphate Kinase from M. jannaschii in complex with IP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 crystals were grown in 1.6M ammonium sulfate, transferred to 1.6M ammonium sulfate, 2mM IP, vapor diffusion, hanging drop, temperature 298K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 2.85 56.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.86 α = 90 b = 100.8 β = 90 c = 87.32 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 2.7 50 99.1 0.074 16.53 5.88 19488 19309 -3 54.186
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) 2.7 2.8 91.8 0.526 2.9 5.81 3076
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.7 40.65 19309 983 99.21 0.227 0.224 0.2276 0.286 0.2163 RANDOM 48.71
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] 0.75 1.72 -2.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.131 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_4_deg 9.517 r_dihedral_angle_1_deg 4.25 r_scangle_it 0.964 r_angle_refined_deg 0.71 r_mcangle_it 0.671 r_scbond_it 0.553 r_mcbond_it 0.366 r_chiral_restr 0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.131 r_dihedral_angle_3_deg 13.341 r_dihedral_angle_4_deg 9.517 r_dihedral_angle_1_deg 4.25 r_scangle_it 0.964 r_angle_refined_deg 0.71 r_mcangle_it 0.671 r_scbond_it 0.553 r_mcbond_it 0.366 r_chiral_restr 0.046 r_bond_refined_d 0.003 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4079 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 40
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction BOS data collection XDS data reduction MOLREP phasing