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Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1186
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MYS PDB ENTRY 3MYS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 100MM TRIS, 200MM LITHIUM SULFATE, 22% PEG 3,350, PH 8.5
Crystal Properties Matthews coefficient Solvent content 2.31 46.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.92 α = 90 b = 108.294 β = 90 c = 139.866 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 293 CCD MARMOSAIC 225 mm CCD 2010-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.1 50 99.8 0.094 9.9 7.5 91912 1
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 2.1 2.14 99.5 0.581 5.4
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 3MYS 2.12 47.94 91598 4595 98.4 0.18 0.177 0.1804 0.25 0.2517 RANDOM 33.03
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] 0.02 0.07 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.67 r_dihedral_angle_4_deg 17.357 r_dihedral_angle_3_deg 12.924 r_scangle_it 7.854 r_scbond_it 5.326 r_dihedral_angle_1_deg 3.968 r_mcangle_it 3.295 r_rigid_bond_restr 3.039 r_mcbond_it 1.998 r_angle_refined_deg 0.882
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.67 r_dihedral_angle_4_deg 17.357 r_dihedral_angle_3_deg 12.924 r_scangle_it 7.854 r_scbond_it 5.326 r_dihedral_angle_1_deg 3.968 r_mcangle_it 3.295 r_rigid_bond_restr 3.039 r_mcbond_it 1.998 r_angle_refined_deg 0.882 r_chiral_restr 0.076 r_gen_planes_refined 0.015 r_bond_refined_d 0.01 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11136 Nucleic Acid Atoms Solvent Atoms 406 Heterogen Atoms 124
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing