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Cytochrome c prime from Alcaligenes xylosoxidans: Ferrous R124A variant with bound NO
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XLH PDB ENTRY 2XLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 AMMONIUM SULPHATE, TRIS PH7.5
Crystal Properties Matthews coefficient Solvent content 2.73 54.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.94 α = 90 b = 52.94 β = 90 c = 182.91 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 PIXEL DECTRIS PILATUS 6M DYNAMICALLY BENDABLE MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 1.07 40 99.1 0.05 22 4 67775 9.3
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 1.07 1.1 99.3 0.48 3.8 3.5
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 2XLH 1.07 45.83 64017 3419 99.15 0.13746 0.13621 0.1453 0.16062 0.1681 RANDOM 8.17
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] -0.16 -0.08 -0.16 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_3_deg 12.091 r_dihedral_angle_4_deg 11.626 r_dihedral_angle_1_deg 5.912 r_scangle_it 3.858 r_scbond_it 2.776 r_mcangle_it 2.104 r_angle_refined_deg 1.749 r_mcbond_it 1.367 r_angle_other_deg 1.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.588 r_dihedral_angle_3_deg 12.091 r_dihedral_angle_4_deg 11.626 r_dihedral_angle_1_deg 5.912 r_scangle_it 3.858 r_scbond_it 2.776 r_mcangle_it 2.104 r_angle_refined_deg 1.749 r_mcbond_it 1.367 r_angle_other_deg 1.023 r_rigid_bond_restr 0.991 r_mcbond_other 0.408 r_chiral_restr 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_gen_planes_other 0.004 r_bond_other_d 0.002 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 943 Nucleic Acid Atoms Solvent Atoms 357 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing