1WA1 | pdb_00001wa1

Crystal Structure Of H313Q Mutant Of Alcaligenes Xylosoxidans Nitrite Reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OE1WWPDB ENTRY 1OE1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5294CRYSTALS OF HIS313GLN NIR WERE GROWN BY THE HANGING-DROP VAPOUR DIFFUSION METHOD AT 21OC. 2ML OF 6-8 MG ML-1 PROTEIN IN 10 MM TRIS-HCL PH 7.1 WAS MIXED WITH AN EQUAL VOLUME OF RESERVOIR SOLUTION CONSISTING OF 25% PEG-MME 550, 10 MM ZINC SULPHATE, 0.1M MES PH 6.5 AND SUSPENDED OVER A 500 ML RESERVOIR. CRYSTALS OF BOTH MUTANTS WERE AN INTENSE BLUE COLOUR AND GREW WITHIN TWO DAYS TO APPROXIMATE DIMENSIONS 0.9 X 0.6 X 0.1 MM IN A RHOMBOHEDRAL MORPHOLOGY.
Crystal Properties
Matthews coefficientSolvent content
3.0559.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.156α = 90
b = 90.156β = 90
c = 143.677γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRRORSMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.1SRSPX14.1

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
11.652098.50.0928.551930
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)
11.651.6997.20.372.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTWWPDB ENTRY 1OE11.6569.01519002652990.1650.1660.180.1910.1921.82
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]
0.910.450.91-1.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.063
r_scangle_it3.307
r_scbond_it2.054
r_angle_refined_deg1.535
r_mcangle_it1.328
r_angle_other_deg0.918
r_mcbond_it0.768
r_symmetry_vdw_other0.327
r_nbd_other0.248
r_nbd_refined0.195
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.063
r_scangle_it3.307
r_scbond_it2.054
r_angle_refined_deg1.535
r_mcangle_it1.328
r_angle_other_deg0.918
r_mcbond_it0.768
r_symmetry_vdw_other0.327
r_nbd_other0.248
r_nbd_refined0.195
r_symmetry_hbond_refined0.166
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.152
r_chiral_restr0.093
r_nbtor_other0.083
r_bond_refined_d0.015
r_gen_planes_other0.011
r_gen_planes_refined0.009
r_bond_other_d0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_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 Atoms2540
Nucleic Acid Atoms
Solvent Atoms352
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing