1WAE

Crystal structure of H129V Mutant of Alcaligenes Xylosoxidans Nitrite Reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NDTPDB ENTRY 1NDT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.5100MM MES BUFFER PH 6.5 200MM ZNSO4, 40-50% PEG550 MME
Crystal Properties
Matthews coefficientSolvent content
3.263

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.206α = 90
b = 91.206β = 90
c = 145.866γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2001-02-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.6SRSPX9.6

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
11.953099.70.05223.535547
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)
11.951.9999.90.42.53

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1NDT1.9530.0131259167099.80.2020.2010.226RANDOM30.52
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]
0.990.490.99-1.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.127
r_dihedral_angle_1_deg5.211
r_scangle_it2.728
r_scbond_it1.698
r_angle_refined_deg1.683
r_mcangle_it1.191
r_symmetry_hbond_refined0.921
r_angle_other_deg0.882
r_mcbond_it0.681
r_nbd_other0.218
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.127
r_dihedral_angle_1_deg5.211
r_scangle_it2.728
r_scbond_it1.698
r_angle_refined_deg1.683
r_mcangle_it1.191
r_symmetry_hbond_refined0.921
r_angle_other_deg0.882
r_mcbond_it0.681
r_nbd_other0.218
r_nbd_refined0.214
r_symmetry_vdw_other0.18
r_symmetry_vdw_refined0.164
r_xyhbond_nbd_refined0.163
r_chiral_restr0.101
r_nbtor_other0.064
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.001
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2545
Nucleic Acid Atoms
Solvent Atoms179
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing