☰ Navigation Tabs
Crystal structure of a naturally folded murine apoptosis inducing factor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GV4 PDB entry 1GV4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 microbatch under oil 7 298 15% PEG 4000, 0.35M KNO3, pH 7.0, microbatch under oil, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.69 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.05 α = 90 b = 80.29 β = 90 c = 419.64 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 103 IMAGE PLATE MAR scanner 345 mm plate mirrors 2008-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.1 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.8 408.25 81.12 0.174 0.174 4.97 61080 49548 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.873 69.45 0.715 0.715 1.7 5.06
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 1GV4 2.95 46.64 71343 43694 2103 83.42 0.25095 0.24861 0.2368 0.29965 0.2944 RANDOM 95.017
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] -6.06 -0.65 6.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.123 r_dihedral_angle_3_deg 20.869 r_dihedral_angle_4_deg 20.288 r_dihedral_angle_1_deg 6.98 r_scangle_it 3.162 r_scbond_it 1.932 r_angle_refined_deg 1.77 r_mcangle_it 1.559 r_mcbond_it 0.991 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.123 r_dihedral_angle_3_deg 20.869 r_dihedral_angle_4_deg 20.288 r_dihedral_angle_1_deg 6.98 r_scangle_it 3.162 r_scbond_it 1.932 r_angle_refined_deg 1.77 r_mcangle_it 1.559 r_mcbond_it 0.991 r_nbtor_refined 0.308 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.173 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.127 r_chiral_restr 0.103 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14482 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 212
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling