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Crystal structure of Plasmodium vivax guanylate kinase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.1 ul Protein, 0.1 ul Crystallization buffer (65% PEG 400, 0.1M MOPS pH 7.5, 0.1M NaNO3, 5mM GMP), VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.96 37.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.535 α = 90 b = 43.535 β = 90 c = 342.8 γ = 120
Symmetry Space Group P 65 2 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 MARMOSAIC 300 mm CCD 2007-06-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97907, 0.97922, 0.91162 SSRL BL9-2
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 1.8 42.84 99.7 0.099 12.1 17.2 19333 29.40802
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 1.8 1.86 98.2 0.612 9.5 1806
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 MAD THROUGHOUT 1.8 37.48 19191 984 99.65 0.201 0.2 0.2188 0.227 0.241 RANDOM 20.737
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] 0.21 0.1 0.21 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.375 r_dihedral_angle_4_deg 15.554 r_dihedral_angle_3_deg 13.563 r_dihedral_angle_1_deg 5.854 r_scangle_it 3.865 r_scbond_it 2.707 r_mcangle_it 1.652 r_angle_refined_deg 1.422 r_mcbond_it 1.335 r_angle_other_deg 0.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.375 r_dihedral_angle_4_deg 15.554 r_dihedral_angle_3_deg 13.563 r_dihedral_angle_1_deg 5.854 r_scangle_it 3.865 r_scbond_it 2.707 r_mcangle_it 1.652 r_angle_refined_deg 1.422 r_mcbond_it 1.335 r_angle_other_deg 0.847 r_mcbond_other 0.279 r_symmetry_vdw_other 0.276 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.201 r_nbd_other 0.19 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.132 r_nbtor_other 0.084 r_chiral_restr 0.079 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1595 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 33
Software Software Software Name Purpose TRUNCATE data reduction DENZO data reduction SCALEPACK data scaling PDB_EXTRACT data extraction MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling SOLVE phasing REFMAC refinement