1GS7 | pdb_00001gs7

Crystal structure of H254F 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
16.540-50% PEG-MME 550, 10MM ZNSO4, 0.1M MES PH6.5, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.4849.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.903α = 90
b = 78.903β = 90
c = 98.423γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHTORROIDAL MIRROR2001-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.5SRSPX9.5

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
11.856098.50.05913.98.529614
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)
11.851.8897.20.3312.42.7

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-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1NDT1.8569.0128098150699.30.1550.1530.194RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.052
r_scbond_it2.795
r_angle_other_deg2.094
r_mcangle_it1.835
r_dihedral_angle_3_deg1.352
r_mcbond_it1.159
r_symmetry_hbond_refined0.246
r_nbtor_other0.219
r_nbd_refined0.21
r_nbd_other0.203
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.052
r_scbond_it2.795
r_angle_other_deg2.094
r_mcangle_it1.835
r_dihedral_angle_3_deg1.352
r_mcbond_it1.159
r_symmetry_hbond_refined0.246
r_nbtor_other0.219
r_nbd_refined0.21
r_nbd_other0.203
r_symmetry_vdw_other0.187
r_symmetry_vdw_refined0.175
r_chiral_restr0.142
r_xyhbond_nbd_other0.114
r_xyhbond_nbd_refined0.109
r_metal_ion_refined0.051
r_bond_refined_d0.025
r_gen_planes_refined0.012
r_gen_planes_other0.005
r_bond_other_d0.001
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_4_deg
r_nbtor_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 Atoms2576
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing