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Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH -703
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZ3 PDB ENTRY 3EZ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 100MM TRIS, 200MM LITHIUM SULFATE, 22% PEG 3,350, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.21 44.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.682 α = 90 b = 107.952 β = 90 c = 140.703 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 298 CCD MARMOSAIC 300 mm CCD SI(111) DOUBLE CRYSTAL MONOCHROMETER 2010-03-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
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 2.6 50 99.7 0.083 28.88 6.1 50497
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 2.6 2.64 99.6 0.305 7.29 6.2
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 3EZ3 2.61 45.58 47716 2554 99.2 0.21 0.208 0.2055 0.253 0.2469 RANDOM 33.77
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] 0.12 0.07 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.564 r_dihedral_angle_4_deg 25.457 r_dihedral_angle_3_deg 18.601 r_dihedral_angle_1_deg 6.859 r_scangle_it 4.781 r_scbond_it 2.915 r_mcangle_it 2.454 r_mcbond_it 1.308 r_angle_refined_deg 1.062 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.564 r_dihedral_angle_4_deg 25.457 r_dihedral_angle_3_deg 18.601 r_dihedral_angle_1_deg 6.859 r_scangle_it 4.781 r_scbond_it 2.915 r_mcangle_it 2.454 r_mcbond_it 1.308 r_angle_refined_deg 1.062 r_chiral_restr 0.087 r_gen_planes_refined 0.018 r_bond_refined_d 0.009 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 11619 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 140
Software Software Software Name Purpose PHASES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling