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High resolution structure of lectin-ike Ox-LDL Receptor 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YPQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 protein 8mg/ml, 10mM Tris-HCl, 150mM NaCl, 1.1 M Sodium Malonate, 0.1M HEPES pH 7, 0.5% v/v Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 2.21 44.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.033 α = 90 b = 49.726 β = 98.57 c = 76.58 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-F 2017-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.984 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.01 75.724 91.2 0.037 0.045 0.025 0.999 12 2.9 105602 12.03
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.01 1.095 59.8 0.601 0.732 0.411 0.627 2.9
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 1YPQ 1.141 16.62 93536 4681 97.6 0.1809 0.1802 0.175 0.1931 0.1874 RANDOM 17.33
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] 0.5836 0.8317 -1.0539 0.4703
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.94 t_omega_torsion 4.84 t_angle_deg 0.99 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.94 t_omega_torsion 4.84 t_angle_deg 0.99 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 2121 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling PHASER phasing Coot model building