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Xray crystal structure determination of H-labeled perdeuterated rubredoxin at 295K
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BRF PDB entry 1BRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 3.8 M sodium/potassium phosphate, hanging drop
Crystal Properties Matthews coefficient Solvent content 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.238 α = 90 b = 35.096 β = 90 c = 43.858 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 295 CCD MAR225 2008-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-BM 1.0 APS 22-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.1 27.4 98.8 8.9 3.7 21725
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 PDB entry 1BRF 1.1 26.99 21692 1107 98.26 0.153 0.152 0.1522 0.165 0.1641 RANDOM 15.095
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] -0.11 0.07 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.316 r_dihedral_angle_3_deg 10.509 r_dihedral_angle_1_deg 5.755 r_scangle_it 3.856 r_sphericity_bonded 3.45 r_scbond_it 2.981 r_mcangle_it 2.6 r_mcbond_it 1.84 r_angle_refined_deg 1.508 r_rigid_bond_restr 1.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.316 r_dihedral_angle_3_deg 10.509 r_dihedral_angle_1_deg 5.755 r_scangle_it 3.856 r_sphericity_bonded 3.45 r_scbond_it 2.981 r_mcangle_it 2.6 r_mcbond_it 1.84 r_angle_refined_deg 1.508 r_rigid_bond_restr 1.439 r_mcbond_other 1.257 r_sphericity_free 1.221 r_angle_other_deg 0.855 r_symmetry_hbond_refined 0.254 r_nbd_refined 0.211 r_nbtor_refined 0.193 r_nbd_other 0.18 r_symmetry_vdw_other 0.151 r_symmetry_vdw_refined 0.119 r_nbtor_other 0.098 r_chiral_restr 0.096 r_xyhbond_nbd_refined 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 419 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ELVES data scaling