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Cytochrome c Nitrite Reductase from Desulfovibrio desulfuricans ATCC 27774: The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA).
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QDB PDB ENTRY 1QDB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 15% W/V PEG 3350, CACL2 0.2M, HEPES PH7.5, 0.1M, 3-(DECYL-METHYLAMMONIUM)PROPANE-1-SULFONATE (ZWITTERGENT 3-10) AS ADDITIVE, pH 7.50
Crystal Properties Matthews coefficient Solvent content 2.34 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.94 α = 90 b = 104.6 β = 90 c = 143.18 γ = 90
Symmetry Space Group P 21 21 21
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 1999-05-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 1.7403,1.7390,0.9919, 0.932 ESRF ID14-4
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 2.3 84.5 94 0.08 11.7 5.6 53690 2 30
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 2.3 2.38 89.8 0.39 2.2 4.9
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD AND MR THROUGHOUT PDB ENTRY 1QDB 2.3 20 51633 522 97.3 0.189 0.189 0.224 0.227 RANDOM 27.7
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] 1.28 1.03 -2.31
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7705 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 440
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing SHARP phasing AMoRE phasing