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Crystal structure of apo form of cyclolavandulyl diphosphate synthase (CLDS) from Streptomyces sp. CL190
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 100mM Tris HCl pH 7.0, 1M sodium citrate tribasic, 200mM NaCl
Crystal Properties Matthews coefficient Solvent content 1.92 36.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.025 α = 90 b = 87.514 β = 90 c = 113.548 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 95 CCD ADSC QUANTUM 270 2014-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 69.32 100 0.117 21.8 7 27009
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 2.03 0.521
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 69.32 25558 1307 99.43 0.19448 0.19235 0.2017 0.23523 0.2405 RANDOM 32.729
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] -0.01 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.007 r_dihedral_angle_4_deg 21.773 r_dihedral_angle_3_deg 15.308 r_dihedral_angle_1_deg 6.333 r_long_range_B_other 6.07 r_long_range_B_refined 6.068 r_scangle_other 4.94 r_scbond_it 3.268 r_scbond_other 3.267 r_mcangle_it 3.208
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.007 r_dihedral_angle_4_deg 21.773 r_dihedral_angle_3_deg 15.308 r_dihedral_angle_1_deg 6.333 r_long_range_B_other 6.07 r_long_range_B_refined 6.068 r_scangle_other 4.94 r_scbond_it 3.268 r_scbond_other 3.267 r_mcangle_it 3.208 r_mcangle_other 3.207 r_mcbond_it 2.411 r_mcbond_other 2.401 r_angle_refined_deg 1.678 r_angle_other_deg 0.991 r_chiral_restr 0.095 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3406 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling AutoSol phasing