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Crystal structure of the reduced, NAD-bound form of 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 VAPOR DIFFUSION, HANGING DROP 6 298 10% PEG 4000, 10% isopropanol, 0.1 M Li citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.907345 57.693363
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.26 α = 90 b = 120.39 β = 90 c = 178.19 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 CCD ADSC QUANTUM 315 mirrors 2002-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.2398 ALS 5.0.2
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 2.24 30.67 95.1 0.042 0.036 6 60034 57099 2 2 46.4
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) 2.24 2.3 85.3 0.333 0.367 3.57 4.6 4363
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1GV4 2.24 30.67 2 2 60041 57099 3035 95.11 0.18861 0.18684 0.22209 0.221 RANDOM 46.368
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] -1.4 1.35 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.435 r_dihedral_angle_4_deg 21.02 r_dihedral_angle_3_deg 16.391 r_dihedral_angle_1_deg 6.053 r_scangle_it 2.551 r_angle_refined_deg 1.671 r_scbond_it 1.546 r_mcangle_it 1.024 r_mcbond_it 0.601 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.435 r_dihedral_angle_4_deg 21.02 r_dihedral_angle_3_deg 16.391 r_dihedral_angle_1_deg 6.053 r_scangle_it 2.551 r_angle_refined_deg 1.671 r_scbond_it 1.546 r_mcangle_it 1.024 r_mcbond_it 0.601 r_nbtor_refined 0.319 r_nbd_refined 0.234 r_xyhbond_nbd_refined 0.203 r_symmetry_hbond_refined 0.164 r_symmetry_vdw_refined 0.124 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 6803 Nucleic Acid Atoms Solvent Atoms 521 Heterogen Atoms 194
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling