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Crystal Structure of the Bacteriophage phi29 gene product 12 N-terminal fragment in complex with 2-(N-cyclohexylamino)ethane sulfonic acid (CHES)
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 10 298 100mM CHES at ~pH 10.0 and 8% PEG3K, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.62 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.841 α = 90 b = 90.841 β = 90 c = 586.952 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 1.03 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 44.24 98.3 0.103 25.233 10.6 62712
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 2.07 100 0.447 11.2 6289
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 44.24 62691 3179 98.16 0.17 0.169 0.1709 0.196 0.1991 RANDOM 23.901
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] 1.16 0.58 1.16 -1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.391 r_dihedral_angle_4_deg 17.072 r_dihedral_angle_3_deg 13.214 r_dihedral_angle_1_deg 6.704 r_scangle_it 3.127 r_scbond_it 2.014 r_angle_refined_deg 1.279 r_mcangle_it 1.118 r_mcbond_it 0.675 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.391 r_dihedral_angle_4_deg 17.072 r_dihedral_angle_3_deg 13.214 r_dihedral_angle_1_deg 6.704 r_scangle_it 3.127 r_scbond_it 2.014 r_angle_refined_deg 1.279 r_mcangle_it 1.118 r_mcbond_it 0.675 r_nbtor_refined 0.304 r_nbd_refined 0.206 r_symmetry_vdw_refined 0.185 r_symmetry_hbond_refined 0.175 r_metal_ion_refined 0.12 r_xyhbond_nbd_refined 0.109 r_chiral_restr 0.097 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4478 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 23
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