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Low Temperature Structure of P22 Tailspike Protein Fragment (109-666), Mutant V125A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VFQ PDB ENTRY 2VFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 10 DROP: 2 MICROLITER 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0, PLUS 3.3 MICROLITER, 10 MG/ML PROTEIN SOLUTION IN 10 MM HEPES, PH 7.0; RESERVOIR: 750 MICOLITER 1.0 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.437 α = 90 b = 120.437 β = 90 c = 120.437 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 MARRESEARCH MIRRORS 2007-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.59 50 98.1 0.05 34.9 12.9 76620 18.4
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 1.59 1.7 90.5 0.1 10.2 3.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VFQ 1.5 49.15 79072 4162 89.3 0.128 0.127 0.1382 0.155 0.1647 RANDOM 10.84
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 35.699 r_dihedral_angle_4_deg 13.727 r_dihedral_angle_3_deg 11.611 r_dihedral_angle_1_deg 6.809 r_scangle_it 4.657 r_scbond_it 3.359 r_mcangle_it 2.073 r_mcbond_it 1.548 r_angle_refined_deg 1.338 r_angle_other_deg 0.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.699 r_dihedral_angle_4_deg 13.727 r_dihedral_angle_3_deg 11.611 r_dihedral_angle_1_deg 6.809 r_scangle_it 4.657 r_scbond_it 3.359 r_mcangle_it 2.073 r_mcbond_it 1.548 r_angle_refined_deg 1.338 r_angle_other_deg 0.916 r_symmetry_vdw_other 0.243 r_nbd_other 0.196 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.173 r_nbtor_refined 0.167 r_xyhbond_nbd_refined 0.135 r_symmetry_hbond_refined 0.125 r_nbtor_other 0.079 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4204 Nucleic Acid Atoms Solvent Atoms 804 Heterogen Atoms 66
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing