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Crystal structure of the bromo domain 1 in human bromodomain containing protein, testis specific (BRDT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NXB PDB entry 2NXB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.20M Na/K tartrate, 20.0% PEG 3350, 10.0% Ethylene glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.34 47.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.935 α = 90 b = 92.679 β = 90 c = 100.107 γ = 90
Symmetry Space Group P 21 21 21
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 225 mm CCD 2007-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97866 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.05 50.063 96.4 0.129 0.129 4.6 6.4 25870 24939
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.16 77.6 0.681 0.681 1 2.9 2857
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2NXB 2.05 50.063 24883 24883 1249 96.38 0.194 0.194 0.191 0.1946 0.259 0.2581 RANDOM 22.732
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] -0.79 0.54 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.254 r_dihedral_angle_3_deg 14.656 r_scangle_it 8.048 r_dihedral_angle_4_deg 7.217 r_scbond_it 6.922 r_dihedral_angle_1_deg 5.799 r_mcangle_it 4.772 r_mcbond_it 4.141 r_mcbond_other 1.974 r_angle_refined_deg 1.517
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.254 r_dihedral_angle_3_deg 14.656 r_scangle_it 8.048 r_dihedral_angle_4_deg 7.217 r_scbond_it 6.922 r_dihedral_angle_1_deg 5.799 r_mcangle_it 4.772 r_mcbond_it 4.141 r_mcbond_other 1.974 r_angle_refined_deg 1.517 r_angle_other_deg 0.993 r_symmetry_vdw_refined 0.295 r_symmetry_vdw_other 0.263 r_nbd_refined 0.193 r_nbtor_refined 0.185 r_nbd_other 0.178 r_xyhbond_nbd_refined 0.159 r_symmetry_hbond_refined 0.15 r_nbtor_other 0.091 r_chiral_restr 0.086 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2562 Nucleic Acid Atoms Solvent Atoms 253 Heterogen Atoms
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection MOSFLM data reduction