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Structure of YncF in complex with dUpNHpp
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XCD PDB ENTRY 2XCD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 0.2M CACL2, 16% PEG 6K, 0.1M HEPES PH7
Crystal Properties Matthews coefficient Solvent content 2.26 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.116 α = 90 b = 99.345 β = 90 c = 99.252 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC CCD 2009-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.85 35.08 99.9 0.01 15.6 9.4 84193 1
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 1.85 1.95 100 0.94 2.4 7.4
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 2XCD 1.85 10 78928 4563 99.9 0.153 0.151 0.1695 0.187 0.2012 RANDOM 16.05
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] 0.38 -0.05 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.392 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_3_deg 15.141 r_dihedral_angle_1_deg 6.897 r_scangle_it 4.608 r_scbond_it 2.97 r_angle_refined_deg 2.007 r_mcangle_it 1.995 r_mcbond_it 1.191 r_angle_other_deg 1.044
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.392 r_dihedral_angle_4_deg 15.995 r_dihedral_angle_3_deg 15.141 r_dihedral_angle_1_deg 6.897 r_scangle_it 4.608 r_scbond_it 2.97 r_angle_refined_deg 2.007 r_mcangle_it 1.995 r_mcbond_it 1.191 r_angle_other_deg 1.044 r_mcbond_other 0.38 r_chiral_restr 0.126 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 6300 Nucleic Acid Atoms Solvent Atoms 792 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing