☰ Navigation Tabs
Human Farnesyl Diphosphate Synthase Complexed with Bisphosphonate BPH-461
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YV5 pdb entry 1YV5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.2 298 10% PEG 2K, 0.5M Phosphate Citrate buffer, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.33 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.783 α = 90 b = 111.783 β = 90 c = 66.525 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 123.2 CCD ADSC QUANTUM 315 2005-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A NSLS X29A
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 2.4 50 98.6 0.1 10.4 12.2 16818
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 2.4 2.49 92 0.412 9.2
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 (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 FREE R pdb entry 1YV5 2.4 30 15918 15918 838 93.7 0.2335 0.2335 0.2138 0.2693 0.2423 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 2868.5
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.086 s_non_zero_chiral_vol 0.023 s_zero_chiral_vol 0.018 s_from_restr_planes 0.0175 s_angle_d 0.016 s_anti_bump_dis_restr 0.007 s_bond_d 0.004 s_similar_dist s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2707 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 31
Software Software Software Name Purpose AMoRE phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling