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X-ray crystal structure determination of fully perdeuterated rubredoxin at 100K
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 2.1 41.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.889 α = 90 b = 34.632 β = 90 c = 43.255 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 100 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 27.04 21196
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 27.04 20120 1076 99.61 0.10736 0.10645 0.1062 0.12485 0.1241 RANDOM 5.227
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] -0.13 0.01 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.558 r_dihedral_angle_3_deg 10.375 r_sphericity_free 8.161 r_dihedral_angle_1_deg 6.021 r_scangle_it 3.504 r_sphericity_bonded 3.465 r_scbond_it 2.5 r_mcangle_it 2.296 r_mcbond_it 2.032 r_angle_refined_deg 1.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.558 r_dihedral_angle_3_deg 10.375 r_sphericity_free 8.161 r_dihedral_angle_1_deg 6.021 r_scangle_it 3.504 r_sphericity_bonded 3.465 r_scbond_it 2.5 r_mcangle_it 2.296 r_mcbond_it 2.032 r_angle_refined_deg 1.612 r_rigid_bond_restr 1.517 r_mcbond_other 1.097 r_angle_other_deg 0.911 r_nbd_refined 0.251 r_symmetry_vdw_other 0.19 r_nbtor_refined 0.188 r_nbd_other 0.183 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.125 r_symmetry_vdw_refined 0.118 r_chiral_restr 0.104 r_nbtor_other 0.09 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 421 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection ELVES data reduction ELVES data scaling