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The crystallographic structure of the Ligand Binding domain of the NR7 nuclear receptor from the amphioxus Branchiostoma lanceolatum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 1.3 M Li2SO4, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.9 35.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.29 α = 90 b = 46.29 β = 90 c = 163.017 γ = 120
Symmetry Space Group P 32 1 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 PIXEL DECTRIS PILATUS 6M 2013-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97625 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 2 40.75 94.5 0.037 0.04 0.015 1 22 6.4 13203 47.73
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 2 2.05 100 0.966 1.046 0.395 0.682 6.7
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 1XIU 2 38.93 13152 609 94.5 0.194 0.192 0.196 0.235 0.2386 RANDOM 69.19
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] -1.6707 -1.6707 3.3414
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.74 t_omega_torsion 2.7 t_angle_deg 1.02 t_bond_d 0.01 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 18.74 t_omega_torsion 2.7 t_angle_deg 1.02 t_bond_d 0.01 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 1846 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 7
Software Software Software Name Purpose BUSTER refinement XSCALE data scaling PHASER phasing PDB_EXTRACT data extraction XDS data reduction