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Crystal structure of polyprenyl synthetase from Streptomyces coelicolor A3(2)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 0.1M PHOSPHATE-CITRATE, PH 4.2, 2M AMMONIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.62 53.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.046 α = 90 b = 68.046 β = 90 c = 147.64 γ = 120
Symmetry Space Group P 31 2 1
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 315 MIRRORS 2010-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 2.2 40 96.1 0.076 10.1 3.7 20789 -5 47.146
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 69.6 0.86 1 2.8
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 2.2 20 19540 652 97.36 0.23264 0.23121 0.2295 0.27513 0.2676 RANDOM 57.074
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] 2.63 1.32 2.63 -3.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.256 r_dihedral_angle_4_deg 19.957 r_dihedral_angle_3_deg 18.736 r_scangle_it 9.525 r_scbond_it 6.415 r_mcangle_it 4.844 r_dihedral_angle_1_deg 4.718 r_mcbond_it 3.182 r_angle_refined_deg 1.183 r_chiral_restr 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.256 r_dihedral_angle_4_deg 19.957 r_dihedral_angle_3_deg 18.736 r_scangle_it 9.525 r_scbond_it 6.415 r_mcangle_it 4.844 r_dihedral_angle_1_deg 4.718 r_mcbond_it 3.182 r_angle_refined_deg 1.183 r_chiral_restr 0.085 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2533 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 30
Software Software Software Name Purpose SHELX model building RESOLVE model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling SHELX phasing RESOLVE phasing