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3Fe-4S, 4Fe-4S plus Zn Acidianus ambivalens ferredoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XER PDB ENTRY 1XER
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION VAPOR DIFFUSION METHOD USING 2 MICROL DROPS OF FRESHLY PURIFIED PROTEIN AT 4.7 MG/ML IN 40 MM POTASSIUM PHOSPHATE PH 6.5 AND 150 NACL, PLUS 2 MICROL OF WELL SOLUTION, 2.4-3.0 M AMMONIUM SULPHATE BUFFERED WITH TRIS-HCL 0.1 M PH 8 AND 0.5 MICROL LAURYLDIMETHYLAMINE-OXIDE (LDAO) 7% (W/V).
Crystal Properties Matthews coefficient Solvent content 1.85 33.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.5 α = 90 b = 117.5 β = 90 c = 50.9 γ = 120
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 CCD 2002-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.01 19.48 99.2 0.08 9.9 2.2 52106
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 2.01 2.07 99.6 0.4 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FREE R-VALUE PDB ENTRY 1XER 2.01 19.48 52097 2491 99.6 0.2148 0.2196 0.2185 0.2729 0.229 THIN SHELLS
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 1 5395
RMS Deviations Key Refinement Restraint Deviation s_similar_adp_cmpnt 0.05 s_zero_chiral_vol 0.036 s_non_zero_chiral_vol 0.032 s_from_restr_planes 0.024 s_angle_d 0.018 s_anti_bump_dis_restr 0.007 s_bond_d 0.006 s_similar_dist 0.004 s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5390 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 112
Software Software Software Name Purpose SHELXL-97 refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing