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New lower bone affinity bisphosphonate drug design for effective use in diseases characterized by abnormal bone resorption
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VF6 PDB ENTRY 2VF6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 1.5 M sodium chloride, 5 mM magnesium chloride, 15% glycerol, 100 mM sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.41 48.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.226 α = 90 b = 112.226 β = 90 c = 65.979 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 300 mm CCD 2007-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9796 APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.59 26.45 89.55 51570 48943 3.5
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 1.59
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 PDB ENTRY 2VF6 1.59 26.45 51574 48943 2625 89.55 0.16763 0.16763 0.16561 0.1747 0.2057 0.2138 RANDOM 23.308
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 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.996 r_dihedral_angle_4_deg 19.431 r_dihedral_angle_3_deg 13.792 r_dihedral_angle_1_deg 5.434 r_angle_refined_deg 2.005 r_angle_other_deg 0.976 r_chiral_restr 0.122 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.996 r_dihedral_angle_4_deg 19.431 r_dihedral_angle_3_deg 13.792 r_dihedral_angle_1_deg 5.434 r_angle_refined_deg 2.005 r_angle_other_deg 0.976 r_chiral_restr 0.122 r_bond_refined_d 0.021 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2718 Nucleic Acid Atoms Solvent Atoms 445 Heterogen Atoms 23
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling