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Crystal structure of Ahp1 from Saccharomyces cerevisiae in reduced form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TP9 PDB ENTRIES 1TP9, 3UMA, 1NM3 AND 2PWJ experimental model PDB 3UMA PDB ENTRIES 1TP9, 3UMA, 1NM3 AND 2PWJ experimental model PDB 1NM3 PDB ENTRIES 1TP9, 3UMA, 1NM3 AND 2PWJ experimental model PDB 2PWJ PDB ENTRIES 1TP9, 3UMA, 1NM3 AND 2PWJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 Protein Solution (40 mg/ml Ahp1 protein, in Milli-Q water containing 10mM DTT) mixed in a 1:1 ratio with the well solution (0.1 M BIS-TRIS pH 5.4, 2.0 M Ammonium Sulfate) Cryoprotected with 20% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 6.39 80.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.049 α = 90 b = 149.049 β = 90 c = 149.049 γ = 90
Symmetry Space Group I 21 3
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 RAYONIX MX-225 2011-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 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 50 100 0.125 9 44.8 37056 37056 29.79
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 2.03 100 0.765 45 1844
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRIES 1TP9, 3UMA, 1NM3 AND 2PWJ 2.004 35.131 1.33 37055 37007 1863 99.87 0.1584 0.1584 0.1576 0.1583 0.1734 0.173 RANDOM 33.7781
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.438 f_angle_d 0.907 f_chiral_restr 0.066 f_bond_d 0.006 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1422 Nucleic Acid Atoms Solvent Atoms 246 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction PHENIX phasing