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Crystal structure of a histone family protein DNA-binding protein from Burkholderia ambifaria
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P71 PDB entry 1P71 as per MoRDa
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 290 6.92 mg/mL BuamA.00144.b.B1.PS37906 with Microlytic MCSG1 screen, condition B8 (25.5% PEG4000, 15% glycerol, 170 mM sodium acetate), cryoprotection: direct, tray 272705 h3, puck ndf9-5
Crystal Properties Matthews coefficient Solvent content 2.46 50.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.21 α = 90 b = 71.4 β = 90 c = 76.73 γ = 90
Symmetry Space Group C 2 2 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 RIGAKU SATURN 944+ 2016-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.85 38.365 99.9 0.064 0.066 0.998 28.26 14.826 9290 30.256
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.9 100 0.506 0.537 0.969 4.72 8.852
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1P71 as per MoRDa 1.85 38.365 1.35 9284 866 99.87 0.2495 0.2447 0.2486 0.2946 0.3004 0 35.5458
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.992 f_angle_d 0.643 f_chiral_restr 0.039 f_bond_d 0.006 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 620 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHENIX refinement PDB_EXTRACT data extraction MoRDa phasing Coot model building