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Cytochrome cd1 Nitrite Reductase, reduced form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AOF PDB ENTRY 1AOF, D1 DOMAIN DIMER
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 ASCORMBATE AND 2.5 UM PMS FROM REDUCTION OF PROTEIN WAS ALSO PRESENT IN CRYSTALLISATION.
Crystal Properties Matthews coefficient Solvent content 4.3 71.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.97 α = 90 b = 127.97 β = 90 c = 264.13 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 2000-06-06 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 2.1 30 99.7 0.077 0.077 17.6 3.8 126324 28.9
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 2.1 2.18 99.6 0.224 0.224 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 1AOF, D1 DOMAIN DIMER 2.1 30 126324 99.7 0.216 0.1969 0.241 RANDOM 28.2
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 32.2 p_staggered_tor 15 p_special_tor 15 p_planar_tor 3.4 p_multtor_nbd 0.237 p_singtor_nbd 0.178 p_xyhbond_nbd 0.152 p_chiral_restr 0.116 p_bond_d 0.09 p_angle_d 0.027
RMS Deviations Key Refinement Restraint Deviation p_transverse_tor 32.2 p_staggered_tor 15 p_special_tor 15 p_planar_tor 3.4 p_multtor_nbd 0.237 p_singtor_nbd 0.178 p_xyhbond_nbd 0.152 p_chiral_restr 0.116 p_bond_d 0.09 p_angle_d 0.027 p_planar_d 0.027 p_plane_restr 0.0057 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 635 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling