2E9E

Crystal structure of the complex of goat lactoperoxidase with Nitrate at 3.25 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GJ1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.2280TRIS HYDROCHLORIDE, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.5451.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.522α = 85.3
b = 72.537β = 84.06
c = 83.983γ = 75.68
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray278IMAGE PLATEMARRESEARCHMirror2006-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.414

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.252095.20.1543.81986319863
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.253.3195.80.2781.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2GJ13.25201986318734100894.850.172140.171230.168680.20343RANDOM18.726
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]
2.51.820.21-0.850.13-2.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.971
r_dihedral_angle_3_deg18.537
r_dihedral_angle_4_deg17.42
r_dihedral_angle_1_deg4.833
r_scangle_it3.379
r_mcangle_it1.919
r_scbond_it1.916
r_angle_refined_deg1.59
r_mcbond_it1.011
r_nbtor_refined0.323
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9508
Nucleic Acid Atoms
Solvent Atoms380
Heterogen Atoms411

Software

Software
Software NamePurpose
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling
AMoREphasing