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Japanin from Rhipicephalus appendiculatus bound to cholesterol: Tetragonal crystal form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QFT PDB ENTRY 1QFT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.1 M IMIDAZOLE PH 7.0 AND 50% V/V 1-METHYL-PENTAN-(2,4)DIOL (MPD).
Crystal Properties Matthews coefficient Solvent content 4.24 71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.33 α = 90 b = 84.33 β = 90 c = 90.52 γ = 90
Symmetry Space Group P 41 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD CYLINDRICAL GRAZING INCIDENCE MIRROR 2010-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.2 84.3 98.9 0.08 15.2 8.6 16985 45.43
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 2.2 2.3 93.2 0.62 2.2 4.5
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 PDB ENTRY 1QFT 2.24 61.7 16158 812 99.3 0.1794 0.1784 0.174 0.1977 0.2037 RANDOM 46.31
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] -2.3529 -2.3529 4.7057
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.44 t_omega_torsion 4.08 t_angle_deg 1.05 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 14.44 t_omega_torsion 4.08 t_angle_deg 1.05 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 1257 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 138
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing