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Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124Q variant with bound NO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E84 PDB ENTRY 1E84
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 AMMONIUM SULPHATE, TRIS PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.77 55.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.728 α = 90 b = 53.728 β = 90 c = 181.223 γ = 120
Symmetry Space Group P 65 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 MARMOSAIC 225 mm CCD MIRRORS 2008-06-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 CLSI 08ID-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 1.17 46.52 95.8 0.06 29 13.3 51845 16.1
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 1.17 1.21 68.4 0.36 2.5 3.8
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 1E84 1.17 46.52 48825 2603 95.2 0.167 0.166 0.1728 0.191 0.1966 RANDOM 15.04
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] 0.43 0.22 0.43 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.874 r_dihedral_angle_4_deg 15.376 r_dihedral_angle_3_deg 14.737 r_dihedral_angle_1_deg 5.706 r_scangle_it 4.637 r_scbond_it 3.491 r_mcangle_it 2.682 r_angle_refined_deg 1.947 r_mcbond_it 1.826 r_rigid_bond_restr 1.518
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.874 r_dihedral_angle_4_deg 15.376 r_dihedral_angle_3_deg 14.737 r_dihedral_angle_1_deg 5.706 r_scangle_it 4.637 r_scbond_it 3.491 r_mcangle_it 2.682 r_angle_refined_deg 1.947 r_mcbond_it 1.826 r_rigid_bond_restr 1.518 r_angle_other_deg 1.146 r_mcbond_other 0.656 r_chiral_restr 0.097 r_bond_refined_d 0.018 r_gen_planes_refined 0.013 r_gen_planes_other 0.006 r_bond_other_d 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 938 Nucleic Acid Atoms Solvent Atoms 202 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing