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Crystal structure of human farnesyl pyrophosphate synthase T210S mutant bound to risedronate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZW5 PDB entry 1ZW5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 0.20 M NH4Cl, 20.0% PEG 6000, 10.0% Ethylene glycol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.44 49.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.47 α = 90 b = 111.47 β = 90 c = 67.603 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 2006-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97956 SLS X10SA
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 1.8 42 99.4 0.063 14.9 4.8 39744 39744 30
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 1.8 1.9 100 0.566 2.4 4.7 5754
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 1ZW5 1.8 30.92 37710 37710 1996 99.23 0.17926 0.17926 0.1778 0.1829 0.20593 0.2088 RANDOM 34.418
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] -1.43 -1.43 2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.582 r_dihedral_angle_4_deg 17.817 r_dihedral_angle_3_deg 13.585 r_scangle_it 6.626 r_scbond_it 5.025 r_dihedral_angle_1_deg 4.672 r_mcangle_it 2.947 r_mcbond_it 2.175 r_angle_refined_deg 1.255 r_angle_other_deg 0.911
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.582 r_dihedral_angle_4_deg 17.817 r_dihedral_angle_3_deg 13.585 r_scangle_it 6.626 r_scbond_it 5.025 r_dihedral_angle_1_deg 4.672 r_mcangle_it 2.947 r_mcbond_it 2.175 r_angle_refined_deg 1.255 r_angle_other_deg 0.911 r_mcbond_other 0.593 r_nbd_refined 0.217 r_symmetry_vdw_other 0.194 r_nbtor_refined 0.187 r_nbd_other 0.174 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.097 r_nbtor_other 0.086 r_chiral_restr 0.07 r_metal_ion_refined 0.019 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 2672 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement MAR345 data collection MOSFLM data reduction SCALA data scaling REFMAC phasing