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Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (monoclinic space group)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 351C PDB ENTRY 351C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9.5 0.1 M CHES PH 9.5, 30% (W/V) PEG 8000
Crystal Properties Matthews coefficient Solvent content 3.06 59.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 138.52 α = 90 b = 81.24 β = 105.17 c = 42.28 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2011-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.1 40.8 94.3 0.15 4.7 2.4 24887 6
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 2.1 2.2 94 0.5 2.3 2.4
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 351C 2.1 40.84 23614 1273 94.06 0.2152 0.21206 0.2113 0.2744 0.2724 RANDOM 26.221
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] 0.45 -0.05 -0.3 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.409 r_dihedral_angle_3_deg 16.677 r_dihedral_angle_1_deg 6.882 r_mcangle_it 2.67 r_angle_refined_deg 1.983 r_scbond_it 1.708 r_mcbond_it 1.661 r_chiral_restr 0.13 r_bond_refined_d 0.025 r_gen_planes_refined 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.409 r_dihedral_angle_3_deg 16.677 r_dihedral_angle_1_deg 6.882 r_mcangle_it 2.67 r_angle_refined_deg 1.983 r_scbond_it 1.708 r_mcbond_it 1.661 r_chiral_restr 0.13 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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_it 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 2348 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing