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Crystal structure of the ancestral soluble variant of the Human Phosphate Binding Protein (HPBP)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V3Q pdb entry 2V3Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 The protein was concentrated at 4mg/mL.
The conditions are 0.2M sodium acetate, 0.1M sodium cacodylate, 25% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.04 α = 90 b = 71.99 β = 103.12 c = 38.98 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 100 PIXEL DECTRIS PILATUS 6M 2013-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97655 SOLEIL PROXIMA 1
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 1.3 99.9103 98.8 0.041 21.36 268471 81625
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 1.3 1.4 99.3 0.275 4.65 3.23
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 2V3Q 1.3 36.1 78327 4123 99.91 0.10864 0.10687 0.1039 0.14253 0.138 RANDOM 13.996
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] 0.35 0.34 -0.24 -0.17
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 72.684 r_dihedral_angle_2_deg 36.279 r_sphericity_bonded 18.957 r_dihedral_angle_4_deg 15.124 r_dihedral_angle_3_deg 11.3 r_rigid_bond_restr 8.745 r_long_range_B_refined 8.674 r_long_range_B_other 8.673 r_dihedral_angle_1_deg 6.069 r_scangle_other 4.692
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 72.684 r_dihedral_angle_2_deg 36.279 r_sphericity_bonded 18.957 r_dihedral_angle_4_deg 15.124 r_dihedral_angle_3_deg 11.3 r_rigid_bond_restr 8.745 r_long_range_B_refined 8.674 r_long_range_B_other 8.673 r_dihedral_angle_1_deg 6.069 r_scangle_other 4.692 r_scbond_other 3.967 r_scbond_it 3.77 r_mcangle_it 2.741 r_mcbond_it 2.414 r_mcbond_other 2.393 r_mcangle_other 2.322 r_angle_refined_deg 1.381 r_angle_other_deg 1.122 r_chiral_restr 0.08 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2748 Nucleic Acid Atoms Solvent Atoms 650 Heterogen Atoms 39
Software Software Software Name Purpose MOLREP phasing REFMAC refinement XDS data reduction XSCALE data scaling