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Crystal structure of cystinosin from Arabidopsis thaliana in complex with Cystine and sybody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7ZK1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 5.5 293 28% PEG 500DME, 100 mM MES-NaOH, pH 5.50, 150 mM K-formate
Crystal Properties Matthews coefficient Solvent content 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 283.372 α = 90 b = 64.065 β = 99.946 c = 55.443 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 PILATUS3 6M 2020-08-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9762 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 3.37 69.78 99.95 0.15 0.79 2 6.1 13144
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.37 3.52 0.1 0.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7ZK1 3.372 69.778 13057 631 92.774 0.251 0.2495 0.2491 0.2795 0.2783 68.309
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] -4.757 -2.371 -8.223 12.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.495 r_dihedral_angle_6_deg 17.383 r_dihedral_angle_1_deg 5.72 r_dihedral_angle_2_deg 5.578 r_lrange_it 2.628 r_lrange_other 2.628 r_mcangle_it 2.045 r_mcangle_other 2.045 r_angle_refined_deg 2.006 r_scangle_it 1.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.495 r_dihedral_angle_6_deg 17.383 r_dihedral_angle_1_deg 5.72 r_dihedral_angle_2_deg 5.578 r_lrange_it 2.628 r_lrange_other 2.628 r_mcangle_it 2.045 r_mcangle_other 2.045 r_angle_refined_deg 2.006 r_scangle_it 1.814 r_scangle_other 1.814 r_mcbond_it 1.388 r_mcbond_other 1.388 r_scbond_it 1.179 r_scbond_other 1.179 r_angle_other_deg 1.036 r_nbd_other 0.441 r_symmetry_xyhbond_nbd_refined 0.434 r_symmetry_nbd_refined 0.396 r_nbd_refined 0.248 r_symmetry_nbd_other 0.226 r_xyhbond_nbd_refined 0.209 r_nbtor_refined 0.195 r_xyhbond_nbd_other 0.163 r_ncsr_local_group_1 0.149 r_symmetry_xyhbond_nbd_other 0.108 r_ncsr_local_group_2 0.105 r_chiral_restr 0.09 r_symmetry_nbtor_other 0.085 r_bond_other_d 0.044 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5898 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing