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Crystal structure of human farnesyl diphosphate synthase (T201A mutant) complexed with Mg and biphosphonate inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QIS PDB entry 2QIS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.2M NH4Cl, 20% PEG 6000, 10% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.3 46.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.531 α = 90 b = 112.531 β = 90 c = 62.919 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 325 mm CCD 2007-12-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97900 SLS X10SA
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 1.95 29.26 99.9 0.114 0.122 9.7 7.2 30040 28451 2
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 1.95 2.06 100 0.612 0.658 2.3 7.2 4311
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2QIS 1.95 27.46 28451 28451 1547 99.96 0.19725 0.19725 0.1948 0.24321 0.2804 RANDOM 25.284
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] -1.8 -1.8 3.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.571 r_dihedral_angle_4_deg 21.538 r_dihedral_angle_3_deg 14.028 r_scangle_it 8.54 r_scbond_it 6.121 r_dihedral_angle_1_deg 5.797 r_mcangle_it 3.548 r_mcbond_it 2.385 r_angle_refined_deg 1.404 r_angle_other_deg 0.979
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.571 r_dihedral_angle_4_deg 21.538 r_dihedral_angle_3_deg 14.028 r_scangle_it 8.54 r_scbond_it 6.121 r_dihedral_angle_1_deg 5.797 r_mcangle_it 3.548 r_mcbond_it 2.385 r_angle_refined_deg 1.404 r_angle_other_deg 0.979 r_mcbond_other 0.714 r_chiral_restr 0.077 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 2639 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing