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T. Brucei Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-1238
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 2.75 55.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.471 α = 90 b = 119.026 β = 112.47 c = 63.47 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 298 CCD ADSC CCD 2014-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A PAL/PLS 7A
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 2.39 85.34 93.3 0.06 14.1 4.4 31850
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 2.4 2.44 92.6 14.1 4.4
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2P1C 2.39 85.34 31850 1668 92.6 0.26344 0.25945 0.2687 0.3338 RANDOM 69.889
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] 0.01 -0.01 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.126 r_dihedral_angle_4_deg 20.404 r_dihedral_angle_3_deg 16.882 r_mcangle_it 6.851 r_dihedral_angle_1_deg 5.221 r_mcbond_it 4.576 r_mcbond_other 4.572 r_scbond_it 4.25 r_angle_other_deg 2.421 r_angle_refined_deg 1.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.126 r_dihedral_angle_4_deg 20.404 r_dihedral_angle_3_deg 16.882 r_mcangle_it 6.851 r_dihedral_angle_1_deg 5.221 r_mcbond_it 4.576 r_mcbond_other 4.572 r_scbond_it 4.25 r_angle_other_deg 2.421 r_angle_refined_deg 1.402 r_chiral_restr 0.07 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_gen_planes_other 0.004 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 184 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction CCP4 phasing