1WA0 | pdb_00001wa0

Crystal Structure Of W138H Mutant Of Alcaligenes Xylosoxidans Nitrite Reductase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OE1PDB ENTRY 1OE1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5294CRYSTALS OF TRP138HIS 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 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
3.0559.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.792α = 90
b = 89.792β = 90
c = 143.462γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORSMSINGLE 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
11.66995.60.0422.45692519.6
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)
11.61.6480.70.432.4

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)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1OE11.669.0154419276895.60.1660.1650.180.1920.19RANDOM23.28
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]
0.790.40.79-1.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.277
r_scangle_it2.967
r_scbond_it1.898
r_angle_refined_deg1.489
r_mcangle_it1.22
r_angle_other_deg0.906
r_mcbond_it0.699
r_symmetry_vdw_other0.304
r_nbd_other0.247
r_nbd_refined0.197
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.277
r_scangle_it2.967
r_scbond_it1.898
r_angle_refined_deg1.489
r_mcangle_it1.22
r_angle_other_deg0.906
r_mcbond_it0.699
r_symmetry_vdw_other0.304
r_nbd_other0.247
r_nbd_refined0.197
r_symmetry_hbond_refined0.189
r_xyhbond_nbd_refined0.171
r_symmetry_vdw_refined0.16
r_chiral_restr0.088
r_nbtor_other0.081
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.008
r_bond_other_d0.002
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 Atoms2541
Nucleic Acid Atoms
Solvent Atoms415
Heterogen Atoms34

Software

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