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Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with BPH-1182
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LDW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 200MM LISO4, 20% PEG3350, 100MM TRIS, PH 8.5, HANGING DROP, TEMPERATURE 291K
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.072 α = 90 b = 117.22 β = 116.2 c = 92.786 γ = 90
Symmetry Space Group P 1 21 1
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 225 mm CCD 2010-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.9787 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 2.7 50 99.5 0.126 9.2 5.3 43920 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 2.7 2.75 97.5 0.561 3.9
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 3LDW 2.7 31.1 38662 2075 92 0.261 0.259 0.2589 0.296 0.2878 RANDOM 47.09
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] 0.08 -0.21 0.21 -0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.845 r_dihedral_angle_3_deg 17.512 r_dihedral_angle_4_deg 16.561 r_dihedral_angle_1_deg 5.706 r_scangle_it 5.307 r_scbond_it 3.005 r_mcangle_it 1.95 r_angle_refined_deg 1.407 r_mcbond_it 0.928 r_chiral_restr 0.105
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.845 r_dihedral_angle_3_deg 17.512 r_dihedral_angle_4_deg 16.561 r_dihedral_angle_1_deg 5.706 r_scangle_it 5.307 r_scbond_it 3.005 r_mcangle_it 1.95 r_angle_refined_deg 1.407 r_mcbond_it 0.928 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 MAIN-CHAIN ANGLE OTHER ATOMS (A**2) SIDE-CHAIN BOND OTHER ATOMS (A**2) SIDE-CHAIN ANGLE OTHER ATOMS (A**2) LONG RANGE B REFINED ATOMS (A**2) LONG RANGE B OTHER ATOMS (A**2) r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10497 Nucleic Acid Atoms Solvent Atoms 161 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling PHASER phasing