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Crystal Structure Analysis of the PHD domain of the Transcription Coactivator Pygophus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 298 1.2M Na Citrate, 0.2M LiSO4, 0.1mM ZnCl2, 50mM Tris, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.079 α = 90 b = 60.079 β = 90 c = 95.242 γ = 90
Symmetry Space Group P 43 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 100 CCD ADSC QUANTUM 4 2005-12-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.286, 1.2826 SPring-8 BL26B2
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 2.7 50 96.5 0.093 6.9 5038 -3
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) 2.7 2.8 81.9 0.27 4.6 413
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.7 20 4772 235 96.94 0.19924 0.1965 0.25495 RANDOM 52.78
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] 2.34 2.34 -4.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 41.322 r_dihedral_angle_2_deg 39.331 r_dihedral_angle_3_deg 23.171 r_dihedral_angle_1_deg 8.349 r_scangle_it 4.342 r_scbond_it 2.666 r_mcangle_it 2.45 r_angle_refined_deg 1.969 r_mcbond_it 1.416 r_symmetry_hbond_refined 0.629
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_4_deg 41.322 r_dihedral_angle_2_deg 39.331 r_dihedral_angle_3_deg 23.171 r_dihedral_angle_1_deg 8.349 r_scangle_it 4.342 r_scbond_it 2.666 r_mcangle_it 2.45 r_angle_refined_deg 1.969 r_mcbond_it 1.416 r_symmetry_hbond_refined 0.629 r_symmetry_vdw_refined 0.412 r_nbtor_refined 0.332 r_nbd_refined 0.289 r_xyhbond_nbd_refined 0.174 r_chiral_restr 0.155 r_bond_refined_d 0.032 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 900 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALEPACK data scaling SOLVE phasing