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T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-1326
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P1C PDB ENTRY 2P1C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.75 298 6% MPD, 0.1 AMMONIUM ACETATE, PH 5.75, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.72 54.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.01 α = 90 b = 117.86 β = 95.8 c = 123.724 γ = 90
Symmetry Space Group I 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 298 CCD ADSC QUANTUM 270 MIRRORS 2013-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A Photon Factory BL-17A
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 2.69 33.29 94.3 0.09 8.7 3 23536
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 2.69 2.84 94.9 0.29 3.7 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2P1C 2.69 32.84 22322 1212 94.08 0.18406 0.18125 0.1878 0.23553 0.2367 RANDOM 43.185
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] -0.03 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.431 r_dihedral_angle_4_deg 19.784 r_dihedral_angle_3_deg 17.068 r_dihedral_angle_1_deg 5.379 r_mcangle_it 4.152 r_scbond_it 3.545 r_mcbond_it 2.629 r_mcbond_other 2.626 r_angle_other_deg 2.422 r_angle_refined_deg 1.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.431 r_dihedral_angle_4_deg 19.784 r_dihedral_angle_3_deg 17.068 r_dihedral_angle_1_deg 5.379 r_mcangle_it 4.152 r_scbond_it 3.545 r_mcbond_it 2.629 r_mcbond_other 2.626 r_angle_other_deg 2.422 r_angle_refined_deg 1.522 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.005 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_it 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 5708 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 phasing