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Cytochrome c' from Alcaligenes xylosoxidans - reduced structure with CO bound to distal 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 CO.
Crystal Properties Matthews coefficient Solvent content 2.71 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.639 α = 90 b = 53.639 β = 90 c = 180.935 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 IMAGE PLATE MARRESEARCH MIRRORS 1999-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A ESRF BM30A
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 1.95 40 98.7 0.066 33.2 9.9 12158 -3 22
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 1.95 2.02 86.8 0.31 5.8
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1CGO 1.95 40 12158 565 98.7 0.203 0.1917 0.258 RANDOM 23
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 25.9 p_staggered_tor 15.3 p_scangle_it 6.836 p_scbond_it 5.583 p_planar_tor 4.5 p_mcangle_it 3.433 p_mcbond_it 2.854 p_multtor_nbd 0.274 p_singtor_nbd 0.172 p_chiral_restr 0.145
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 25.9 p_staggered_tor 15.3 p_scangle_it 6.836 p_scbond_it 5.583 p_planar_tor 4.5 p_mcangle_it 3.433 p_mcbond_it 2.854 p_multtor_nbd 0.274 p_singtor_nbd 0.172 p_chiral_restr 0.145 p_xyhbond_nbd 0.145 p_planar_d 0.036 p_angle_d 0.034 p_plane_restr 0.0282 p_bond_d 0.016 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 925 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing