3N8F | pdb_00003n8f

Crystal structure of the complex of goat lactoperoxidase with thiocyanate at 3.2 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.22800.2M Ammonium nitrate 20%w/v PEG 3350, PH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.5451.51

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 RU3001.5418

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
13.252595.20.0613.82090120901
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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2OJV3.2524.981976718756101194.580.209540.20530.210.248270.3RANDOM23.727
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]
2.1420.39-0.470.13-2.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.592
r_dihedral_angle_3_deg16.713
r_dihedral_angle_4_deg15.414
r_dihedral_angle_1_deg6.053
r_scangle_it1.273
r_angle_refined_deg1.246
r_scbond_it0.69
r_mcangle_it0.684
r_symmetry_hbond_refined0.467
r_mcbond_it0.365
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.592
r_dihedral_angle_3_deg16.713
r_dihedral_angle_4_deg15.414
r_dihedral_angle_1_deg6.053
r_scangle_it1.273
r_angle_refined_deg1.246
r_scbond_it0.69
r_mcangle_it0.684
r_symmetry_hbond_refined0.467
r_mcbond_it0.365
r_symmetry_vdw_refined0.324
r_nbtor_refined0.309
r_nbd_refined0.237
r_metal_ion_refined0.23
r_xyhbond_nbd_refined0.172
r_chiral_restr0.086
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9514
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms356

Software

Software
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling