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Crystal structure of IspD from Bacillus subtilis at 1.80 Angstroms resolution, crystal form I
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.2M Trimethylamine N-oxide dehydrate, 0.1M Tris, pH 8.5, 20% (v/v)Polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 2.18 43.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.339 α = 90 b = 77.951 β = 90 c = 91.473 γ = 90
Symmetry Space Group P 21 21 21
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 315r 2014-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U
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 1.8 60 99 0.052 21.7 3.6 42387
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 1.8 1.86 100 0.349 3.7 3.6
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 2YC3 1.8 59.33 40202 2142 98.69 0.18145 0.17958 0.191 0.2155 0.2235 RANDOM 28.023
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] 0.86 -0.37 -0.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.306 r_dihedral_angle_4_deg 19.702 r_dihedral_angle_3_deg 13.923 r_long_range_B_refined 7.575 r_long_range_B_other 7.379 r_dihedral_angle_1_deg 6.377 r_scangle_other 5.395 r_mcangle_it 3.535 r_mcangle_other 3.534 r_scbond_it 3.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.306 r_dihedral_angle_4_deg 19.702 r_dihedral_angle_3_deg 13.923 r_long_range_B_refined 7.575 r_long_range_B_other 7.379 r_dihedral_angle_1_deg 6.377 r_scangle_other 5.395 r_mcangle_it 3.535 r_mcangle_other 3.534 r_scbond_it 3.368 r_scbond_other 3.367 r_mcbond_it 2.384 r_mcbond_other 2.379 r_angle_refined_deg 1.672 r_angle_other_deg 0.957 r_chiral_restr 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3634 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing