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Crystal structure of FAD binding domain of Erv1 from Saccharomyces cerevisiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OQC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 300 25% polyethylene glycol 3350, 0.2M Ammonium acetate, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties Matthews coefficient Solvent content 2.07 40.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.553 α = 90 b = 46.599 β = 90 c = 58.88 γ = 90
Symmetry Space Group P 2 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 2010-01-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.979 SSRF BL17U
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 50 99.7 0.064 30.9 10.4 7555 7532 -3
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 2.07 100 0.238 10.68 10.5 727
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1OQC 2 50 7224 7185 346 99.46 0.19399 0.19228 0.22874 0.2467 RANDOM 35.154
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] 3.15 -2.18 -0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.029 r_dihedral_angle_4_deg 19.364 r_dihedral_angle_3_deg 16.284 r_dihedral_angle_1_deg 6.218 r_scangle_it 5.687 r_scbond_it 3.435 r_mcangle_it 2.141 r_angle_refined_deg 1.753 r_mcbond_it 1.074 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.029 r_dihedral_angle_4_deg 19.364 r_dihedral_angle_3_deg 16.284 r_dihedral_angle_1_deg 6.218 r_scangle_it 5.687 r_scbond_it 3.435 r_mcangle_it 2.141 r_angle_refined_deg 1.753 r_mcbond_it 1.074 r_chiral_restr 0.111 r_bond_refined_d 0.017 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 890 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 53
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction SCALA data scaling