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Crystal structure of the HsdR subunit of the EcoR124I restriction enzyme with the C-terminal domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2W00 2w00, 5j3n experimental model PDB 5J3N 2w00, 5j3n
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 1 UL OF PROTEIN IN 20 MM PHOSPHATE PH 7.5, 100 MM KCL, 5 MM ATP WAS MIXED WITH 2 UL OF RESERVOIR, CONTAINING 0.2 M LI2SO4, 8 % PEG 20K, 8 % PEG 550 MME, 1.5 MM DTT
Crystal Properties Matthews coefficient Solvent content 2.68 54.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.91 α = 90 b = 129.922 β = 90 c = 161.01 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 MARRESEARCH 2006-10-20 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.987 EMBL/DESY, HAMBURG X12
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.6 20 100 18.2 9.4 80316
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2w00, 5j3n 2.6 19.968 1.33 80202 977 99.93 0.2035 0.2027 0.2035 0.2638 0.2578
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 5.413 f_angle_d 1.008 f_chiral_restr 0.053 f_bond_d 0.009 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14917 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 64
Software Software Software Name Purpose PHENIX refinement DENZO data reduction SCALEPACK data scaling Auto-Rickshaw phasing