2NQX

Crystal Structure of bovine lactoperoxidase with iodide ions at 2.9A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.4549.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.53α = 90
b = 80.549β = 103.74
c = 78.031γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray290IMAGE PLATEMAR scanner 345 mm platemirror2006-09-25MSINGLE 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
12.92598.60.176.5130261302638.9
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)
12.9397.10.4062.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2IPS2.9525130261302668198.50.1980.196030.2363RANDOM25.324
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]
0.1-0.91-0.730.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.057
r_dihedral_angle_3_deg16.57
r_dihedral_angle_4_deg14.941
r_dihedral_angle_1_deg4.233
r_mcangle_it3.046
r_mcbond_it2.122
r_scangle_it1.726
r_angle_refined_deg1.212
r_scbond_it1.024
r_symmetry_hbond_refined0.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.057
r_dihedral_angle_3_deg16.57
r_dihedral_angle_4_deg14.941
r_dihedral_angle_1_deg4.233
r_mcangle_it3.046
r_mcbond_it2.122
r_scangle_it1.726
r_angle_refined_deg1.212
r_scbond_it1.024
r_symmetry_hbond_refined0.412
r_nbtor_refined0.314
r_nbd_refined0.219
r_xyhbond_nbd_refined0.141
r_symmetry_vdw_refined0.112
r_chiral_restr0.091
r_metal_ion_refined0.083
r_bond_refined_d0.008
r_gen_planes_refined0.004
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 Atoms4770
Nucleic Acid Atoms
Solvent Atoms151
Heterogen Atoms193

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
AUTOMARdata reduction
SCALEPACKdata scaling
AMoREphasing