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Arabidopsis thaliana IspD apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W77 PDB ENTRY 1W77
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 293 50 mM HEPES, 50 mM CdSO4, 800 mM KAc, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 46.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.64 α = 90 b = 73.64 β = 90 c = 224.39 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 PSI PILATUS 6M 2012-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 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 1.5 30 99.7 0.039 23 5.3 37739 2
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 1.5 1.6 99.9 0.567 3.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1W77 1.5 10 37895 36000 1895 99.7 0.178 0.177 0.2001 0.194 0.2162 RANDOM 27.55
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] 0.54 0.27 0.54 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.571 r_dihedral_angle_3_deg 14.967 r_dihedral_angle_4_deg 7.725 r_dihedral_angle_1_deg 6.007 r_angle_refined_deg 2.663 r_chiral_restr 0.169 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.571 r_dihedral_angle_3_deg 14.967 r_dihedral_angle_4_deg 7.725 r_dihedral_angle_1_deg 6.007 r_angle_refined_deg 2.663 r_chiral_restr 0.169 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 1681 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 16
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling