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Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase PV003920 from Plasmodium vivax
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VH8 PDB entry 1VH8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 293 25% PEG 3350, 0.1 M Citric acid pH 3.5, 2 mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.661 α = 90 b = 79.661 β = 90 c = 79.661 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV 2007-05-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 1.5418
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 2.26 50 100 0.105 0.07 8.9 18.3 8156 8156 53.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.26 2.34 99.9 0.8958 0.7177 1.57 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 PDB entry 1VH8 2.26 39.84 8159 8156 376 99.96 0.20664 0.20405 0.25746 0.218 RANDOM 45.102
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.39 r_dihedral_angle_3_deg 19.282 r_dihedral_angle_4_deg 12.583 r_dihedral_angle_1_deg 8.023 r_scangle_it 4.695 r_scbond_it 3.047 r_mcangle_it 1.94 r_angle_refined_deg 1.835 r_mcbond_it 1.121 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.39 r_dihedral_angle_3_deg 19.282 r_dihedral_angle_4_deg 12.583 r_dihedral_angle_1_deg 8.023 r_scangle_it 4.695 r_scbond_it 3.047 r_mcangle_it 1.94 r_angle_refined_deg 1.835 r_mcbond_it 1.121 r_nbtor_refined 0.308 r_symmetry_hbond_refined 0.22 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.123 r_bond_refined_d 0.021 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 1138 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 1
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction