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L16I mutant of cytochrome c prime from Alcaligenes xylosoxidans: Ferrous state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2YLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 2.2M Ammonium sulfate, 0.1 M HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.02 55.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.52 α = 90 b = 53.52 β = 90 c = 179.682 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-F 2015-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.1 44.8 98.7 0.064 0.998 9.6 5.5 61939
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 1.1 1.12 94.8 0.652 1.5 4.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2YLI 1.12 10 51996 42.5 0.153 0.1616 0.181 0.1623 RANDOM 18.1983
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]
RMS Deviations Key Refinement Restraint Deviation s_angle_d 325 s_zero_chiral_vol 53 s_non_zero_chiral_vol 8 s_approx_iso_adps 0.121 s_similar_adp_cmpnt 0.041 s_anti_bump_dis_restr 0.035 s_bond_d 0.015 s_from_restr_planes 0.004 s_similar_dist s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 940 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 43
Software Software Software Name Purpose Aimless data scaling SHELXDE phasing PDB_EXTRACT data extraction XDS data reduction PHASER phasing