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Cytochrome cd1 Nitrite Reductase, oxidised from from tetragonal crystals
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1H9X PDB ENTRY 1H9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9 HANGING DROP USING 2.1 M AMMONIUM SULPHATE AND 100 MM CHES PH 7.0 1 MM ASCORBATE AND 2.5 UM PMS FROM REDUCTION OF PROTEIN WAS ALSO PRESENT IN CRYSTALLISATION. CRYSTALS WERE GROWN UNDER STRICTLY ANAEROBIC CONDITIONS. THE ENZYME WAS OXIDISED IN THE CRYSTAL BY ALLOWING AIR TO DIFFUSE INTO THE DROP
Crystal Properties Matthews coefficient Solvent content 4.3 71.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 128.305 α = 90 b = 128.305 β = 90 c = 264.825 γ = 90
Symmetry Space Group P 43 21 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 2000-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 MAX II I711
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.5 30 98.1 0.062 0.062 17.6 3.1 74676 35.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.59 91.2 0.28 0.28 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 1H9X 2.5 30 74676 98.1 0.226 0.192 0.258 RANDOM 39.7
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]
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 32.9 p_special_tor 15 p_staggered_tor 12.9 p_planar_tor 1.9 p_multtor_nbd 0.261 p_singtor_nbd 0.186 p_xyhbond_nbd 0.173 p_chiral_restr 0.14 p_planar_d 0.019 p_angle_d 0.017
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 32.9 p_special_tor 15 p_staggered_tor 12.9 p_planar_tor 1.9 p_multtor_nbd 0.261 p_singtor_nbd 0.186 p_xyhbond_nbd 0.173 p_chiral_restr 0.14 p_planar_d 0.019 p_angle_d 0.017 p_bond_d 0.013 p_plane_restr 0.0041 p_angle_deg p_hb_or_metal_coord p_mcbond_it p_mcangle_it p_scbond_it p_scangle_it p_xhyhbond_nbd p_orthonormal_tor
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8204 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 204
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling