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1.2 A Crystal Structure of Housefly cytochrome c at pH 11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B4Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.7 291 Concentrated protein in 0.5 mM EDTA, 20 mM Tris-HCL pH 7.5 was mixed with an equal volume of precipitant containing 0.1 M Glycine pH 10.0 and 28% w/v Polyethylene Glycol Monomethyl Ether 2000 and allowed to vapor diffuse against a reservoir of the same precipitant. Before cryoprotection and freezing, the crystal was transferred to a well containing 0.1 M CAPS pH 11.0 and 28% w/v Polyethylene Glycol Monomethyl Ether 2000. The crystal fractured, and a fragment was ued for collection.
Crystal Properties Matthews coefficient Solvent content 2.11 41.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.876 α = 90 b = 58.634 β = 106.772 c = 51.674 γ = 90
Symmetry Space Group P 1 21 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 CCD ADSC QUANTUM 270 2015-03-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.9804 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.2 38 91.83 0.088 0.097 0.04 0.994 10.4 5.36 55990 -3 13.85
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.24 45.23 0.459 0.534 0.264 0.779 1.6 2.41
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.2 37.81 0.93 55798 1574 92.28 0.1273 0.1262 0.131 0.165 0.1683 21.76
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 f_dihedral_angle_d 13.7568 f_angle_d 1.1051 f_chiral_restr 0.0738 f_plane_restr 0.0128 f_bond_d 0.0086
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1642 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 89
Software Software Software Name Purpose PHENIX refinement PHENIX refinement DENZO data reduction SCALEPACK data scaling PHASER phasing