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Sphingomonas yanoikuyae B1 ferredoxin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FQT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.8 288 0.05M phosphate buffer, 0.1M citric acid, 1.6M ammonium sulfate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.84 56.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.064 α = 90 b = 62.064 β = 90 c = 238.436 γ = 120
Symmetry Space Group P 65 2 2
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 2004-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.03320 NSLS X6A
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 1.62 49 70.4 0.125 8.1 4.74 25261 25261
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) 1.62 1.68 7.2 0.539 1.2 1.24 254
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 (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 THROUGHOUT 1FQT 1.9 9.5 20863 20863 1059 93.28 0.196 0.196 0.193 0.207 0.24 0.2507 RANDOM 15.189
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] 1.26 0.63 1.26 -1.9
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.69 r_dihedral_angle_3_deg 14.525 r_dihedral_angle_1_deg 7.364 r_dihedral_angle_4_deg 4.678 r_scangle_it 3.357 r_scbond_it 2.464 r_angle_refined_deg 1.935 r_mcangle_it 1.314 r_mcbond_it 1.061 r_angle_other_deg 0.972
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.69 r_dihedral_angle_3_deg 14.525 r_dihedral_angle_1_deg 7.364 r_dihedral_angle_4_deg 4.678 r_scangle_it 3.357 r_scbond_it 2.464 r_angle_refined_deg 1.935 r_mcangle_it 1.314 r_mcbond_it 1.061 r_angle_other_deg 0.972 r_symmetry_hbond_refined 0.354 r_symmetry_vdw_refined 0.346 r_mcbond_other 0.233 r_symmetry_vdw_other 0.222 r_xyhbond_nbd_refined 0.209 r_nbd_refined 0.202 r_nbd_other 0.188 r_nbtor_refined 0.179 r_chiral_restr 0.102 r_nbtor_other 0.088 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_metal_ion_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1547 Nucleic Acid Atoms Solvent Atoms 193 Heterogen Atoms 39
Software Software Software Name Purpose d*TREK data scaling AMoRE phasing REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection d*TREK data reduction