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Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from the isoprenoid biosynthetic pathway of Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GX1 PDB ENTRY 1GX1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 18% PEG3350, 100mM MES, 200mM Ammonium Dihydrogen Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.01 59.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.795 α = 90 b = 135.795 β = 90 c = 135.795 γ = 90
Symmetry Space Group I 41 3 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 ADSC QUANTUM 315 mirrors 2006-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.0358 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 19.6 100 0.057 7 19.6 9624 9624 56
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 89.67 0.422 3.3 602
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 (All) 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 1GX1 2.3 19.6 9150 9150 468 98.3 0.2 0.2 0.198 0.2009 0.251 0.2493 RANDOM 4.3
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 38.17 r_dihedral_angle_3_deg 16.609 r_dihedral_angle_4_deg 14.949 r_dihedral_angle_1_deg 8.186 r_scangle_it 2.662 r_scbond_it 1.841 r_angle_refined_deg 1.507 r_mcangle_it 1.356 r_mcbond_it 1.232 r_angle_other_deg 0.984
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.17 r_dihedral_angle_3_deg 16.609 r_dihedral_angle_4_deg 14.949 r_dihedral_angle_1_deg 8.186 r_scangle_it 2.662 r_scbond_it 1.841 r_angle_refined_deg 1.507 r_mcangle_it 1.356 r_mcbond_it 1.232 r_angle_other_deg 0.984 r_symmetry_vdw_other 0.26 r_nbd_other 0.199 r_nbd_refined 0.193 r_nbtor_refined 0.163 r_mcbond_other 0.136 r_xyhbond_nbd_refined 0.128 r_symmetry_hbond_refined 0.104 r_symmetry_vdw_refined 0.101 r_chiral_restr 0.089 r_nbtor_other 0.087 r_metal_ion_refined 0.034 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1220 Nucleic Acid Atoms Solvent Atoms 68 Heterogen Atoms 28
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection MOLREP phasing