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Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MRO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 293 50 mM HEPES, 50 mM CdSO4, 800 mM KAc
Crystal Properties Matthews coefficient Solvent content 2.36 47.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.99 α = 90 b = 74.99 β = 90 c = 221.72 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 100 PIXEL DECTRIS PILATUS3 S 6M 2012-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
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 1.9 50 100 0.04 30.6 11 19377
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 1.9 2 100 0.4 5.7
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 5MRO 1.9 15 18358 966 99.7 0.20544 0.20389 0.2094 0.23461 0.2323 RANDOM 47.614
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] -0.49 -0.25 -0.49 1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.157 r_sphericity_free 21.161 r_dihedral_angle_3_deg 17.048 r_dihedral_angle_4_deg 12.19 r_sphericity_bonded 5.866 r_dihedral_angle_1_deg 5.833 r_long_range_B_refined 3.104 r_long_range_B_other 3.096 r_mcangle_other 2.704 r_mcangle_it 2.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.157 r_sphericity_free 21.161 r_dihedral_angle_3_deg 17.048 r_dihedral_angle_4_deg 12.19 r_sphericity_bonded 5.866 r_dihedral_angle_1_deg 5.833 r_long_range_B_refined 3.104 r_long_range_B_other 3.096 r_mcangle_other 2.704 r_mcangle_it 2.701 r_mcbond_it 2.431 r_mcbond_other 2.428 r_scangle_other 2.339 r_scbond_it 2.086 r_scbond_other 2.084 r_angle_refined_deg 1.41 r_rigid_bond_restr 1.378 r_angle_other_deg 0.947 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1629 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing