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Crystal Structure of the Bacteriophage phi29 gene product 12 C-terminal fragment in complex with ATP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 100mM Bis-Tris at pH 7.0, 20% PEG4K, 10%v/v MPD, 10mM MgCl2 and 10mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.86 57.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.211 α = 90 b = 85.211 β = 90 c = 85.211 γ = 90
Symmetry Space Group P 21 3
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 2.5 26.95 98.6 0.042 56.473 10.8 7288
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 2.5 2.59 100 0.55 11.1 730
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 3GQH 2.5 26.95 7244 334 98.54 0.267 0.264 0.2588 0.334 0.317 RANDOM 43.909
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 r_dihedral_angle_2_deg 41.054 r_dihedral_angle_3_deg 18.461 r_dihedral_angle_4_deg 9.56 r_dihedral_angle_1_deg 8.459 r_scangle_it 2.998 r_scbond_it 1.827 r_angle_refined_deg 1.43 r_mcangle_it 1.171 r_mcbond_it 0.687 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.054 r_dihedral_angle_3_deg 18.461 r_dihedral_angle_4_deg 9.56 r_dihedral_angle_1_deg 8.459 r_scangle_it 2.998 r_scbond_it 1.827 r_angle_refined_deg 1.43 r_mcangle_it 1.171 r_mcbond_it 0.687 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.267 r_nbd_refined 0.231 r_xyhbond_nbd_refined 0.177 r_symmetry_hbond_refined 0.117 r_chiral_restr 0.108 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1274 Nucleic Acid Atoms Solvent Atoms 3 Heterogen Atoms 32
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