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Crystal structure of rubredoxin reductase from Pseudomonas aeruginosa.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XHC PDB ENTRY 1XHC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5% PEG 1000, 40% PEG 300, TRIS-CL PH 7.0
Crystal Properties Matthews coefficient Solvent content 4.1 70
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.602 α = 90 b = 119.602 β = 90 c = 158.064 γ = 120
Symmetry Space Group P 61 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 MARRESEARCH 2006-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 2.4 50 98.1 0.07 11.8 3.6 25303 2.7
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 2.4 2.49 82.9 0.34 2.7 2.8
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 1XHC 2.4 103.7 25303 1333 99.6 0.168 0.166 0.1704 0.202 0.2041 RANDOM 33.37
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] -0.47 -0.23 -0.47 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.928 r_dihedral_angle_4_deg 21.153 r_dihedral_angle_3_deg 14.987 r_dihedral_angle_1_deg 6.003 r_scangle_it 2.896 r_scbond_it 1.887 r_angle_refined_deg 1.493 r_mcangle_it 1.079 r_mcbond_it 0.708 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.928 r_dihedral_angle_4_deg 21.153 r_dihedral_angle_3_deg 14.987 r_dihedral_angle_1_deg 6.003 r_scangle_it 2.896 r_scbond_it 1.887 r_angle_refined_deg 1.493 r_mcangle_it 1.079 r_mcbond_it 0.708 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.201 r_xyhbond_nbd_refined 0.151 r_symmetry_hbond_refined 0.128 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2824 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing