☰ Navigation Tabs
Crystal structure of the Nitrosomonas europaea Rh protein complexed with carbon dioxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B9Y PDB entry 3B9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 14.5% PEG 2000 MME, 1 mM EDTA, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.41 63.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.434 α = 90 b = 100.434 β = 90 c = 143.467 γ = 120
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 ADSC QUANTUM 315 2007-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-1 0.91837 SSRL BL9-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.85 41.631 97.9 0.076 0.076 7.48 3.4 46080 45094 2 17.744
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.85 1.9 95.9 0.523 0.425 1.6 3.1 3309
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 3B9Y 1.85 41.631 45092 2275 97.85 0.166 0.166 0.1661 0.179 0.1796 RANDOM 23.102
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] 0.52 0.26 0.52 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.708 r_dihedral_angle_3_deg 12.55 r_dihedral_angle_4_deg 9.729 r_dihedral_angle_1_deg 4.287 r_angle_refined_deg 1.002 r_scangle_it 0.958 r_mcangle_it 0.626 r_scbond_it 0.626 r_mcbond_it 0.352 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.708 r_dihedral_angle_3_deg 12.55 r_dihedral_angle_4_deg 9.729 r_dihedral_angle_1_deg 4.287 r_angle_refined_deg 1.002 r_scangle_it 0.958 r_mcangle_it 0.626 r_scbond_it 0.626 r_mcbond_it 0.352 r_nbtor_refined 0.298 r_nbd_refined 0.182 r_symmetry_vdw_refined 0.132 r_symmetry_hbond_refined 0.08 r_xyhbond_nbd_refined 0.076 r_chiral_restr 0.07 r_bond_refined_d 0.007 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2942 Nucleic Acid Atoms Solvent Atoms 321 Heterogen Atoms 47
Software Software Software Name Purpose MOSFLM data reduction DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection SCALA data scaling MOLREP phasing