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Crystal structure of the pre-mature bacteriophage phi29 gene product 12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GQ7 PDB entries 3GQ7, 3GQH experimental model PDB 3GQH PDB entries 3GQ7, 3GQH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 3.0 M Sodium Acetate at pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.27 71.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.889 α = 90 b = 95.889 β = 90 c = 795.391 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 2008-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 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 2.15 49.27 88 0.146 17.143 15.6 68349
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 2.15 2.23 57 0.446 6
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 PDB entries 3GQ7, 3GQH 2.15 49.27 50808 2533 65.5 0.262 0.261 0.291 0.27 RANDOM 48.27
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] 2.21 1.11 2.21 -3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.845 r_dihedral_angle_3_deg 15.9 r_dihedral_angle_4_deg 15.556 r_dihedral_angle_1_deg 6.333 r_scangle_it 2.4 r_scbond_it 1.546 r_angle_refined_deg 1.088 r_mcangle_it 0.942 r_mcbond_it 0.575 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.845 r_dihedral_angle_3_deg 15.9 r_dihedral_angle_4_deg 15.556 r_dihedral_angle_1_deg 6.333 r_scangle_it 2.4 r_scbond_it 1.546 r_angle_refined_deg 1.088 r_mcangle_it 0.942 r_mcbond_it 0.575 r_nbtor_refined 0.3 r_nbd_refined 0.189 r_metal_ion_refined 0.189 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.155 r_xyhbond_nbd_refined 0.11 r_chiral_restr 0.075 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5746 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 34
Software Software Software Name Purpose PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling