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Crystal Structure of the Bacteriophage phi29 gene product 12 N-terminal fragment in complex with cobalt ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GQ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 298 100mM Tris-base at pH 10.5 and 8% PEG3K. Apo crystals were obtained by soaking the crystals in a mother liquid containing 10mM EDTA. The cobalt derivative was obtained by back soaking the apo-crystals in a mother liquid containing 10mM cobalt ions, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.52 65.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.741 α = 90 b = 89.741 β = 90 c = 584.795 γ = 120
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 300 mm CCD 2008-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.98 APS 23-ID-D
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 2.1 43.88 99.5 0.099 31.667 8.5 53528
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 2.1 2.18 100 0.555 8.7 5279
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3GQ7 2.1 43.88 53508 2708 99.49 0.182 0.18 0.1815 0.222 0.2238 RANDOM 29.128
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] 1.83 0.92 1.83 -2.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.907 r_dihedral_angle_4_deg 16.783 r_dihedral_angle_3_deg 13.29 r_dihedral_angle_1_deg 6.996 r_scangle_it 3.174 r_scbond_it 2.058 r_angle_refined_deg 1.377 r_mcangle_it 1.121 r_mcbond_it 0.691 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.907 r_dihedral_angle_4_deg 16.783 r_dihedral_angle_3_deg 13.29 r_dihedral_angle_1_deg 6.996 r_scangle_it 3.174 r_scbond_it 2.058 r_angle_refined_deg 1.377 r_mcangle_it 1.121 r_mcbond_it 0.691 r_nbtor_refined 0.308 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.187 r_symmetry_hbond_refined 0.167 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.098 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4473 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 7
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling