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Geranylgeranyl diphosphate synthase from Sinapis alba
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10 pH 10.00
Crystal Properties Matthews coefficient Solvent content 3.29 62.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.81 α = 90 b = 71.81 β = 90 c = 127.85 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 MARRESEARCH 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 2 50 99.1 0.06 17.2 8.5 26607 -3
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 2.2 96.5 0.31 5.5 7
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 SIRAS THROUGHOUT 2 45 25071 1328 99.8 0.196 0.195 0.1972 0.23 0.2346 RANDOM 21.69
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] -1.13 -0.56 -1.13 1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.067 r_dihedral_angle_3_deg 16.334 r_dihedral_angle_4_deg 11.182 r_dihedral_angle_1_deg 5.423 r_scangle_it 3.58 r_scbond_it 2.639 r_angle_refined_deg 1.563 r_mcangle_it 1.495 r_mcbond_it 1.239 r_angle_other_deg 1.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.067 r_dihedral_angle_3_deg 16.334 r_dihedral_angle_4_deg 11.182 r_dihedral_angle_1_deg 5.423 r_scangle_it 3.58 r_scbond_it 2.639 r_angle_refined_deg 1.563 r_mcangle_it 1.495 r_mcbond_it 1.239 r_angle_other_deg 1.054 r_mcbond_other 0.29 r_symmetry_vdw_other 0.279 r_nbd_refined 0.236 r_symmetry_vdw_refined 0.214 r_nbd_other 0.19 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.1 r_nbtor_other 0.089 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other 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 1912 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling