☰ Navigation Tabs
2C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I52 PDB ENTRY 1I52
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M HEPES PH 7.5, 0.05 M CADMIUM SULFATE, 1 M SODIUM ACETATE, 0.04 COPPER(II) CHLORIDE
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.496 α = 90 b = 74.496 β = 90 c = 223.026 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 160 CCD ADSC CCD MIRRORS 2003-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 29.75 99.8 0.05 22.3 16.9 16508
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 2.07 99.4 0.43 2.8
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1I52 2 27.95 15674 833 99.8 0.237 0.232 0.349 RANDOM 50.92
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] 0.05 0.02 0.05 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.588 r_dihedral_angle_3_deg 21.323 r_dihedral_angle_4_deg 21.091 r_scangle_it 18.78 r_scbond_it 16.556 r_mcangle_it 11.302 r_dihedral_angle_1_deg 9.782 r_mcbond_it 9.567 r_angle_refined_deg 1.652 r_nbtor_refined 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.588 r_dihedral_angle_3_deg 21.323 r_dihedral_angle_4_deg 21.091 r_scangle_it 18.78 r_scbond_it 16.556 r_mcangle_it 11.302 r_dihedral_angle_1_deg 9.782 r_mcbond_it 9.567 r_angle_refined_deg 1.652 r_nbtor_refined 0.33 r_symmetry_vdw_refined 0.324 r_xyhbond_nbd_refined 0.299 r_nbd_refined 0.298 r_symmetry_hbond_refined 0.269 r_chiral_restr 0.117 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1640 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling BEAST phasing