2DWT

Cu-containing nitrite reductase at pH 6.0 with bound nitrite


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZV2PDB ENTRY 1ZV2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298Tris, MgCl2, NaNO2, PEG 4000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2946.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.74α = 90
b = 74.74β = 90
c = 153.146γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2005-04-27MSINGLE 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
11.924.7199.30.060.067.23.224972
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)
11.921000.3630.3631.83.13664

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1ZV21.924.7124965127099.210.2010.1990.235RANDOM33.106
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]
-1.55-0.78-1.552.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.707
r_dihedral_angle_4_deg18.564
r_dihedral_angle_3_deg14.444
r_dihedral_angle_1_deg7.642
r_scangle_it3.304
r_scbond_it2.507
r_angle_refined_deg1.878
r_mcangle_it1.622
r_mcbond_it1.131
r_nbtor_refined0.319
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.707
r_dihedral_angle_4_deg18.564
r_dihedral_angle_3_deg14.444
r_dihedral_angle_1_deg7.642
r_scangle_it3.304
r_scbond_it2.507
r_angle_refined_deg1.878
r_mcangle_it1.622
r_mcbond_it1.131
r_nbtor_refined0.319
r_nbd_refined0.213
r_symmetry_vdw_refined0.199
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.153
r_chiral_restr0.133
r_symmetry_metal_ion_refined0.04
r_metal_ion_refined0.032
r_bond_refined_d0.02
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2530
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms8

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing