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Structure of the SPX domain of the human phosphate transporter XPR1 in complex with a sulfate ion
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 298 1.4M AmSO4, 0.1M Tris, 16% glycerol
Crystal Properties Matthews coefficient Solvent content 2.56 51.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.95 α = 90 b = 80.32 β = 90 c = 97.86 γ = 90
Symmetry Space Group P 21 21 21
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 2M 2013-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976250 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 2.43 50 99.9 0.067 1 16.65 7.6 20166 -3 65.09
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 2.43 2.49 99.8 1.75 7.3
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 5IIG 2.43 25.28 20143 1007 99.88 0.2034 0.2014 0.2116 0.2438 0.2588 RANDOM 91.79
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] -12.6918 21.1993 -8.5075
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.33 t_omega_torsion 2.62 t_angle_deg 1.04 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 19.33 t_omega_torsion 2.62 t_angle_deg 1.04 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3039 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 10
Software Software Software Name Purpose BUSTER refinement XDS data reduction XDS data scaling PHASER phasing