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Crystal Structure of the Bacteriophage Phi29 Gene Product 12 N-terminal Fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10.5 298 100mM Tris-base at ~pH10.5 and 8% PEG3K, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.53 65.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.879 α = 90 b = 89.879 β = 90 c = 585.44 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 MAR CCD 165 mm 2008-04-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-ID-B 1.07 APS 14-ID-B
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 2.05 50 99.8 0.077 28.259 8.3 58072
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 2.05 2.12 99.6 0.315 8.4 5660
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.05 43.81 58017 2940 99.77 0.159 0.158 0.161 0.19 0.1925 RANDOM 21.551
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] 0.59 0.3 0.59 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.781 r_dihedral_angle_4_deg 16.812 r_dihedral_angle_3_deg 12.629 r_dihedral_angle_1_deg 6.549 r_scangle_it 2.746 r_scbond_it 1.757 r_angle_refined_deg 1.227 r_mcangle_it 0.96 r_mcbond_it 0.596 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.781 r_dihedral_angle_4_deg 16.812 r_dihedral_angle_3_deg 12.629 r_dihedral_angle_1_deg 6.549 r_scangle_it 2.746 r_scbond_it 1.757 r_angle_refined_deg 1.227 r_mcangle_it 0.96 r_mcbond_it 0.596 r_nbtor_refined 0.301 r_nbd_refined 0.201 r_metal_ion_refined 0.19 r_symmetry_vdw_refined 0.174 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 4488 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling