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Crystal structure of human geranylgeranyl pyrophosphate synthase bound to GGPP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other GGPS1 MONOMER BUILT INTO SAD-PHASED MAP (UNPUBLISHED)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 25% PEG 3350, 0.2M MG FORMATE, pH 5.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.51 51.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.248 α = 90 b = 141.248 β = 90 c = 211.705 γ = 90
Symmetry Space Group P 41 21 2
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 MARMOSAIC 225 mm CCD 2005-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.008 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.7 47.08 99.9 12 7.7 59513 59513
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.72 100 2.83 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT GGPS1 MONOMER BUILT INTO SAD-PHASED MAP (UNPUBLISHED) 2.7 47.08 57186 57186 2211 99.98 0.20434 0.20434 0.20246 0.2073 0.25329 0.2589 RANDOM 43.886
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] 0.04 0.04 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.744 r_dihedral_angle_4_deg 18.695 r_dihedral_angle_3_deg 17.149 r_dihedral_angle_1_deg 5.521 r_scangle_it 1.855 r_angle_refined_deg 1.389 r_scbond_it 1.167 r_angle_other_deg 0.947 r_mcangle_it 0.735 r_mcbond_it 0.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.744 r_dihedral_angle_4_deg 18.695 r_dihedral_angle_3_deg 17.149 r_dihedral_angle_1_deg 5.521 r_scangle_it 1.855 r_angle_refined_deg 1.389 r_scbond_it 1.167 r_angle_other_deg 0.947 r_mcangle_it 0.735 r_mcbond_it 0.438 r_symmetry_vdw_other 0.286 r_symmetry_vdw_refined 0.247 r_nbd_refined 0.232 r_nbtor_refined 0.191 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.165 r_symmetry_hbond_refined 0.161 r_metal_ion_refined 0.103 r_mcbond_other 0.094 r_nbtor_other 0.089 r_chiral_restr 0.07 r_xyhbond_nbd_other 0.055 r_bond_refined_d 0.014 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_other 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 13713 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 176
Software Software Software Name Purpose PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling