☰ Navigation Tabs
Crystal structure of a decaprenyl diphosphate synthase from Rhodobacter capsulatus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 294 100mM MES pH 6.5, 30% PEG MME 5K, 200mM ammonium sulfate, vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.459 α = 90 b = 90.245 β = 125.76 c = 80.167 γ = 90
Symmetry Space Group C 1 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 2010-01-26 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 Merge I (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 1.9 30 99.9 0.064 0.064 13 6.1 56604 29.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.93 100 0.479 0.479 3 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.9 20 56161 56071 2837 99.8 0.194 0.193 0.207 0.221 0.237 RANDOM 46.95
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] -2.9 -1.89 1.9 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.998 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 16.251 r_dihedral_angle_1_deg 5.008 r_scangle_it 4.082 r_scbond_it 2.711 r_mcangle_it 1.609 r_angle_refined_deg 1.507 r_angle_other_deg 1.012 r_mcbond_it 0.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.998 r_dihedral_angle_4_deg 17.452 r_dihedral_angle_3_deg 16.251 r_dihedral_angle_1_deg 5.008 r_scangle_it 4.082 r_scbond_it 2.711 r_mcangle_it 1.609 r_angle_refined_deg 1.507 r_angle_other_deg 1.012 r_mcbond_it 0.924 r_mcbond_other 0.251 r_chiral_restr 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4795 Nucleic Acid Atoms Solvent Atoms 305 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SHELXCD phasing SHELXE model building