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Structure of human REV7 in complex with a human REV3 fragment in a tetragonal crystal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ABD PDB ENTRY 3ABD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 8% PEG 20000, 8% PEG 550 MME, 0.8M sodium formate, 0.1M tris-HCl pH 8.5
, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.73 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.517 α = 90 b = 76.517 β = 90 c = 118.524 γ = 90
Symmetry Space Group P 41 21 2
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 QUANTUM 315 2007-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
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 2.6 50 96.9 0.057 13.2 11076
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 2.6 2.69 81.8 0.314 3.1
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 3ABD 2.6 20 10491 526 100 0.24242 0.24046 0.2378 0.28149 0.3047 RANDOM 30.66
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] -5.09 -5.09 10.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.987 r_dihedral_angle_4_deg 30.346 r_dihedral_angle_3_deg 20.198 r_dihedral_angle_1_deg 7.302 r_angle_other_deg 4.119 r_scangle_it 2.317 r_angle_refined_deg 1.782 r_scbond_it 1.59 r_mcangle_it 1.097 r_mcbond_it 0.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.987 r_dihedral_angle_4_deg 30.346 r_dihedral_angle_3_deg 20.198 r_dihedral_angle_1_deg 7.302 r_angle_other_deg 4.119 r_scangle_it 2.317 r_angle_refined_deg 1.782 r_scbond_it 1.59 r_mcangle_it 1.097 r_mcbond_it 0.9 r_symmetry_vdw_refined 0.542 r_symmetry_vdw_other 0.368 r_nbd_refined 0.275 r_nbd_other 0.273 r_nbtor_refined 0.213 r_xyhbond_nbd_refined 0.186 r_mcbond_other 0.132 r_nbtor_other 0.119 r_chiral_restr 0.083 r_xyhbond_nbd_other 0.043 r_bond_refined_d 0.018 r_symmetry_hbond_refined 0.015 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1746 Nucleic Acid Atoms Solvent Atoms 14 Heterogen Atoms
Software Software Software Name Purpose SERGUI data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling