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Crystal Structure of PF11_0147
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N9X pdb entry 3N9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 22% PEG 3350, 0.175 M disodium tartrate,
2 mM AMPPNP,
4 mM MgCl2,
2 mM TCEP,
20% glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.26 45.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.388 α = 90 b = 107.355 β = 109.65 c = 70.787 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU SATURN A200 2010-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 2.3 50 95.4 0.05 7.2 3.7 39641 37818 1 1 53.2
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 2.3 2.34 85.7 0.338 3 1719
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 pdb entry 3N9X 2.3 50 39772 37792 1906 95.02 0.2254 0.2231 0.2174 0.2681 0.2627 RANDOM 48.6944
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] -5.06 -0.53 3.96 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.76 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_3_deg 16.197 r_dihedral_angle_1_deg 5.863 r_scangle_it 2.213 r_scbond_it 1.361 r_angle_refined_deg 1.28 r_mcangle_it 1.112 r_angle_other_deg 0.863 r_mcbond_it 0.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.76 r_dihedral_angle_4_deg 17.323 r_dihedral_angle_3_deg 16.197 r_dihedral_angle_1_deg 5.863 r_scangle_it 2.213 r_scbond_it 1.361 r_angle_refined_deg 1.28 r_mcangle_it 1.112 r_angle_other_deg 0.863 r_mcbond_it 0.601 r_mcbond_other 0.089 r_chiral_restr 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5808 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 62
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing