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Crystal structure of an AT-rich interactive domain-containing protein 3A (ARID3A) from Homo sapiens at 2.21 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2KK0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 20.00% PEG-6000, 0.1M Citrate pH 5.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.95 36.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.924 α = 108.12 b = 43.092 β = 82.22 c = 44.894 γ = 98.17
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 Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 2.21 42.467 92 0.128 7.31 11361 -3 29.192
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 2.21 2.29 94.3 0.568 2.5
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 2kk0 2.21 42.467 11357 534 92.49 0.1832 0.1822 0.1921 0.2017 0.2099 RANDOM 32.9359
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] 3.2135 -3.3636 1.7811 -3.051 1.9209 -0.1625
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.91 t_omega_torsion 2.51 t_angle_deg 0.93 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 2.91 t_omega_torsion 2.51 t_angle_deg 0.93 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 1981 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction PHASER phasing XSCALE data scaling BUSTER-TNT refinement XDS data reduction BUSTER refinement