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Cytochrome c' from Alcaligenes xylosoxidans - reduced structure with NO bound to proximal side of heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CGO PDB ENTRY 1CGO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 HANGING DROP VAPOUR DIFFUSION. PROTEIN AT CONCENTRATION 8 MG/ML WAS MIXED WITH AN EQUAL VOLUME OF WELL SOLUTION CONSISTING OF 55-65% SATURATED AMMONIUM SULFATE IN 100 MM HEPES BUFFER AT PH 7.5. REDUCED USING MOTHER LIQUOR CONTAINING 20 MM SODIUM DITHIONITE, THEN INCUBATED FOR 6 DAYS IN MOTHER LIQUOR SATURATED WITH NO.
Crystal Properties Matthews coefficient Solvent content 2.71 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.035 α = 90 b = 53.035 β = 90 c = 180.993 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 ADSC CCD MIRRORS 2000-01-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.35 40 98.8 0.039 39.8 6.8 33925 -3 16
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 1.35 1.37 93.1 0.227 3.9
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1CGO 1.35 40 33925 1732 98.8 0.194 0.1884 0.22 RANDOM 18
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 p_transverse_tor 27.4 p_staggered_tor 12.8 p_planar_tor 4.3 p_scangle_it 3.959 p_scbond_it 2.867 p_mcangle_it 1.623 p_mcbond_it 1.238 p_multtor_nbd 0.267 p_singtor_nbd 0.17 p_xyhbond_nbd 0.14
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 27.4 p_staggered_tor 12.8 p_planar_tor 4.3 p_scangle_it 3.959 p_scbond_it 2.867 p_mcangle_it 1.623 p_mcbond_it 1.238 p_multtor_nbd 0.267 p_singtor_nbd 0.17 p_xyhbond_nbd 0.14 p_chiral_restr 0.092 p_planar_d 0.03 p_angle_d 0.024 p_plane_restr 0.0239 p_bond_d 0.011 p_angle_deg p_hb_or_metal_coord p_xhyhbond_nbd p_orthonormal_tor p_special_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 927 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing