1H9Y

Cytochrome cd1 Nitrite Reductase, reduced form complexed to CN


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H9XPDB ENTRY 1H9X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP9HANGING 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 coefficientSolvent content
4.371.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 127.573α = 90
b = 127.573β = 90
c = 263.201γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2000-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I711MAX III711

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.42097.90.0860.08616.43.28342743.6
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)RedundancyNumber Unique Reflections (All)
12.42.49930.2870.2873.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1H9X2.4208342799.70.2380.269RANDOM40.2
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
KeyRefinement Restraint Deviation
p_transverse_tor31.6
p_special_tor15
p_staggered_tor14.9
p_planar_tor3
p_chiral_restr0.98
p_multtor_nbd0.243
p_singtor_nbd0.184
p_xyhbond_nbd0.16
p_bond_d0.08
p_angle_d0.026
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor31.6
p_special_tor15
p_staggered_tor14.9
p_planar_tor3
p_chiral_restr0.98
p_multtor_nbd0.243
p_singtor_nbd0.184
p_xyhbond_nbd0.16
p_bond_d0.08
p_angle_d0.026
p_planar_d0.024
p_plane_restr0.0047
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 AtomsNumber
Protein Atoms8107
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms202

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling