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Human farnesyl diphosphate synthase complexed with Mg and risedronate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 293 40% PEG 300, 0.1M phosphate-citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.4 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.946 α = 90 b = 110.946 β = 90 c = 70.264 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 ADSC QUANTUM 4 2005-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.16 ALS 8.3.1
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 2 70.2 99.9 0.092 0.092 8.7 30242 30212 34.3
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 2.11 100 2.2 8.6 4319
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 MOLECULAR REPLACEMENT THROUGHOUT 1UBV 2 52.34 28656 28467 1529 99.34 0.20765 0.20765 0.20549 0.2133 0.24888 0.2483 RANDOM 25.087
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] -3.2 -3.2 6.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.077 r_dihedral_angle_4_deg 18.511 r_dihedral_angle_3_deg 14.515 r_scangle_it 6.838 r_dihedral_angle_1_deg 5.484 r_scbond_it 5.361 r_mcangle_it 3.248 r_mcbond_it 2.122 r_angle_refined_deg 1.531 r_angle_other_deg 0.824
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.077 r_dihedral_angle_4_deg 18.511 r_dihedral_angle_3_deg 14.515 r_scangle_it 6.838 r_dihedral_angle_1_deg 5.484 r_scbond_it 5.361 r_mcangle_it 3.248 r_mcbond_it 2.122 r_angle_refined_deg 1.531 r_angle_other_deg 0.824 r_mcbond_other 0.54 r_nbd_refined 0.218 r_nbtor_refined 0.195 r_nbd_other 0.17 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.159 r_symmetry_vdw_other 0.151 r_metal_ion_refined 0.142 r_symmetry_hbond_refined 0.132 r_nbtor_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 2650 Nucleic Acid Atoms Solvent Atoms 82 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing