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Crystal structure of SPF45 UHM domain with cyclic peptide inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PEH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 50mM MES pH 6, 70% MPD
Crystal Properties Matthews coefficient Solvent content 2.5 50.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.6 α = 90 b = 73.59 β = 97.9 c = 45.01 γ = 90
Symmetry Space Group P 1 21 1
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 2M-F 2012-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1 SLS X06DA
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 2.22 38.13 98 0.07603 14.61 5.1 11806 21.85
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 2.22 2.3 88 0.2116 5.29 4 1034
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2PEH 2.22 38.13 11192 590 98.2 0.1972 0.1812 0.2444 0.243 RANDOM 23.814
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] 1.18 -2.85 -0.98 0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.185 r_dihedral_angle_4_deg 25.943 r_dihedral_angle_3_deg 15.009 r_dihedral_angle_1_deg 7.635 r_mcangle_it 2.671 r_angle_refined_deg 1.759 r_mcbond_it 1.678 r_mcbond_other 1.676 r_angle_other_deg 1.273 r_chiral_restr 0.093
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.185 r_dihedral_angle_4_deg 25.943 r_dihedral_angle_3_deg 15.009 r_dihedral_angle_1_deg 7.635 r_mcangle_it 2.671 r_angle_refined_deg 1.759 r_mcbond_it 1.678 r_mcbond_other 1.676 r_angle_other_deg 1.273 r_chiral_restr 0.093 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.006 r_bond_other_d 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1725 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction