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Arabidopsis thaliana IspD Asp262Ala Mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MRN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 50 mM HEPES, 50 mM CdSO4, 800 mM KAc
Crystal Properties Matthews coefficient Solvent content 2.36 47.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.53 α = 90 b = 74.53 β = 90 c = 224.16 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 2012-12-08 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 2.2 50 99.3 0.054 23.7 8.4 12488
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 2.3 94.9 0.563 4.2
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 5MRN 2.2 15 11813 622 99.08 0.18244 0.18057 0.1852 0.21726 0.2212 RANDOM 56.729
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] 0.16 0.08 0.16 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.463 r_sphericity_free 28.502 r_dihedral_angle_3_deg 14.831 r_dihedral_angle_4_deg 8.741 r_sphericity_bonded 7.032 r_dihedral_angle_1_deg 5.452 r_long_range_B_refined 4.551 r_long_range_B_other 4.345 r_mcangle_other 3.64 r_mcangle_it 3.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.463 r_sphericity_free 28.502 r_dihedral_angle_3_deg 14.831 r_dihedral_angle_4_deg 8.741 r_sphericity_bonded 7.032 r_dihedral_angle_1_deg 5.452 r_long_range_B_refined 4.551 r_long_range_B_other 4.345 r_mcangle_other 3.64 r_mcangle_it 3.633 r_scangle_other 3.095 r_mcbond_it 2.781 r_mcbond_other 2.764 r_scbond_it 2.626 r_scbond_other 2.622 r_rigid_bond_restr 1.593 r_angle_refined_deg 1.209 r_angle_other_deg 0.876 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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 1672 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing