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Crystal structure of the Cytochrome C552 from moderate thermophilic bacterium, hydrogenophilus thermoluteolus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 30% (w/v) polyethylene glycol 4000, 0.1M Mes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.2 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.25 α = 90 b = 58.413 β = 90 c = 56.315 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE RIGAKU RAXIS IV++ confocal mirror optics 2004-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.2 50 94.4 0.08 17.65 4.4 4086 4086 2 2
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) 2.2 2.28 75.3 0.184 4.67 3.9 314
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 2.2 9.74 2 3898 4025 378 94.16 0.181 0.184 0.181 0.1559 0.218 0.1539 RANDOM 20.466
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] 0.03 -0.1 0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.356 r_dihedral_angle_3_deg 20.803 r_dihedral_angle_1_deg 7.789 r_scangle_it 4.486 r_dihedral_angle_4_deg 4.477 r_mcangle_it 4.014 r_scbond_it 3.07 r_mcbond_it 2.574 r_angle_refined_deg 1.434 r_nbtor_refined 0.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.356 r_dihedral_angle_3_deg 20.803 r_dihedral_angle_1_deg 7.789 r_scangle_it 4.486 r_dihedral_angle_4_deg 4.477 r_mcangle_it 4.014 r_scbond_it 3.07 r_mcbond_it 2.574 r_angle_refined_deg 1.434 r_nbtor_refined 0.326 r_nbd_refined 0.297 r_symmetry_vdw_refined 0.275 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.119 r_bond_refined_d 0.023 r_gen_planes_refined 0.017 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 600 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing