1OE1

Atomic Resolution Structure of the Wildtype Native Nitrite Reductase from Alcaligenes xylosoxidans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HAUPDB ENTRY 1HAU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.540-50% PEG-MME 550, 0.1M MES PH 6.5, 10MM CUSO4
Crystal Properties
Matthews coefficientSolvent content
2.449.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.725α = 90
b = 78.725β = 90
c = 98.885γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2001-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.2SRSPX14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.046096.60.07519.110.6167110
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.041.0693.10.332.32.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1HAU1.0460162462324597.90.11750.11930.1416RANDOM
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]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
183106
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.099
s_zero_chiral_vol0.093
s_approx_iso_adps0.087
s_from_restr_planes0.0352
s_similar_adp_cmpnt0.035
s_angle_d0.032
s_bond_d0.017
s_rigid_bond_adp_cmpnt0.006
s_similar_dist
s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2548
Nucleic Acid Atoms
Solvent Atoms464
Heterogen Atoms15

Software

Software
Software NamePurpose
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing