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Second Bromodomain of cdg4_1340 from Cryptosporidium parvum, complexed with bromosporine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PY6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 The protein was crystallized at 293 K in 2.5M ammonium sulfate, 0.1 M bis-tris propane pH 7.0. Bromosporine (ethyl (3-methyl-6-{4-methyl-3-[(methylsulfonyl)amino]phenyl}[1,2,4]triazolo[4,3- b]pyridazin-8-yl)carbamate) was added (final concentration of 1 mM)directly to the concentrated protein immediately prior to setting up the crystallization plate
Crystal Properties Matthews coefficient Solvent content 3.95 68.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.119 α = 90 b = 186.124 β = 90 c = 195.176 γ = 90
Symmetry Space Group F 2 2 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 CCD MARMOSAIC 300 mm CCD 2016-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97600 APS 22-ID
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 2.4 33.67 99.8 0.1 0.108 0.041 0.996 18 7.1 22425 57.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 98.6 0.639 0.8 6.9
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 4PY6 2.4 32.54 22371 1107 99.9 0.226 0.225 0.2328 0.256 0.26 RANDOM 67.55
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] -7.7804 11.833 -4.0526
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.22 t_omega_torsion 3.08 t_angle_deg 0.61 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 16.22 t_omega_torsion 3.08 t_angle_deg 0.61 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 1961 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 61
Software Software Software Name Purpose Aimless data scaling BUSTER refinement PDB_EXTRACT data extraction PHASER phasing