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XPF from Aeropyrum pernix
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BGW SEPARATE DOMAINS FROM PART-REFINED PDB ENTRY 2BGW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 65% V/V MPD, 0.1M TRIS-HCL PH8.0. SITTING DROPS.
Crystal Properties Matthews coefficient Solvent content 2.32 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 210.325 α = 90 b = 42.752 β = 121.42 c = 118.736 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 3.2 38.93 99.9 0.06 10.6 3.6 52273 50
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 3.2 3.37 100 0.31 2.4 3.7
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT SEPARATE DOMAINS FROM PART-REFINED PDB ENTRY 2BGW 3.2 25 14575 768 100 0.221 0.216 0.32 RANDOM 60.83
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] 1.02 0.05 -1.34 0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.367 r_dihedral_angle_3_deg 21.259 r_dihedral_angle_4_deg 20.758 r_dihedral_angle_1_deg 7.1 r_scangle_it 1.985 r_angle_refined_deg 1.703 r_scbond_it 1.164 r_mcangle_it 0.762 r_mcbond_it 0.436 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.367 r_dihedral_angle_3_deg 21.259 r_dihedral_angle_4_deg 20.758 r_dihedral_angle_1_deg 7.1 r_scangle_it 1.985 r_angle_refined_deg 1.703 r_scbond_it 1.164 r_mcangle_it 0.762 r_mcbond_it 0.436 r_nbtor_refined 0.326 r_symmetry_vdw_refined 0.298 r_symmetry_hbond_refined 0.291 r_nbd_refined 0.271 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_refined 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_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 5905 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing