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Crystal Structure of Plasmodium vivax geranylgeranylpyrophosphate synthase PVX_092040 with zoledronate and IPP bound
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20 % PEG3350
0.2 M Li2SO4
0.1 M Tris 8.5
5% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.266 α = 90 b = 109.696 β = 90 c = 139.529 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 270 2007-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9197 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.304 25 100 0.184 0.127 10.667 7.3 72585 72515 44.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.304 2.49 99.9 0.689 1.4 7 7173
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.304 24.43 75940 72250 3633 95.13 0.229 0.229 0.226 0.291 0.2822 RANDOM 24.385
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] -0.01 0.1 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.799 r_dihedral_angle_4_deg 20.629 r_dihedral_angle_3_deg 17.325 r_dihedral_angle_1_deg 6.116 r_scangle_it 2.648 r_scbond_it 1.819 r_angle_refined_deg 1.649 r_mcangle_it 1.105 r_mcbond_it 0.661 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.799 r_dihedral_angle_4_deg 20.629 r_dihedral_angle_3_deg 17.325 r_dihedral_angle_1_deg 6.116 r_scangle_it 2.648 r_scbond_it 1.819 r_angle_refined_deg 1.649 r_mcangle_it 1.105 r_mcbond_it 0.661 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.264 r_nbd_refined 0.215 r_xyhbond_nbd_refined 0.181 r_chiral_restr 0.115 r_symmetry_hbond_refined 0.098 r_metal_ion_refined 0.075 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11546 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 158
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection