1ZV2

Cu-containing nitrite reductase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.4295PEG4000, MgCl2, Tris, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
3.160.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.381α = 90
b = 72.381β = 90
c = 147.509γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.007MAX III711

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
11.7426.798.60.0659.729034-3.7
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)
11.741.811000.342.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1NIF1.7426.72756927569146597.640.156670.15470.19367RANDOM14.943
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]
-0.02-0.01-0.020.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.419
r_dihedral_angle_4_deg17.852
r_dihedral_angle_3_deg13.033
r_dihedral_angle_1_deg6.977
r_scangle_it3.071
r_scbond_it2.03
r_angle_refined_deg1.438
r_mcangle_it1.147
r_mcbond_it0.776
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.419
r_dihedral_angle_4_deg17.852
r_dihedral_angle_3_deg13.033
r_dihedral_angle_1_deg6.977
r_scangle_it3.071
r_scbond_it2.03
r_angle_refined_deg1.438
r_mcangle_it1.147
r_mcbond_it0.776
r_nbtor_refined0.31
r_nbd_refined0.2
r_symmetry_hbond_refined0.192
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.125
r_chiral_restr0.099
r_metal_ion_refined0.072
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2522
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing