7Y3U

Crystal structure of the complex of Lactoperoxidase with Nitric oxide at 2.50A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6LRN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.82980.2M cacl2, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.347.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.731α = 90
b = 93.173β = 91.2
c = 82.319γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2019-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONRRCAT INDUS-2 BEAMLINE PX-BL210.97947RRCAT INDUS-2PX-BL21

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.548.911990.0780.9977.83.942834
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5998.70.8060.6381.23.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6LRN2.548.86442372210598.9240.2220.2190.277459.307
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]
-0.154-0.015-0.0880.243
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.804
r_dihedral_angle_3_deg16.038
r_dihedral_angle_4_deg14.488
r_lrange_it12.434
r_lrange_other12.434
r_dihedral_angle_1_deg7.749
r_mcangle_it7.285
r_mcangle_other7.284
r_scangle_it6.353
r_scangle_other6.353
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.804
r_dihedral_angle_3_deg16.038
r_dihedral_angle_4_deg14.488
r_lrange_it12.434
r_lrange_other12.434
r_dihedral_angle_1_deg7.749
r_mcangle_it7.285
r_mcangle_other7.284
r_scangle_it6.353
r_scangle_other6.353
r_mcbond_it4.569
r_mcbond_other4.568
r_scbond_it3.939
r_scbond_other3.938
r_angle_other_deg2.453
r_angle_refined_deg1.506
r_symmetry_nbd_refined0.241
r_symmetry_nbd_other0.218
r_nbd_other0.21
r_nbd_refined0.209
r_xyhbond_nbd_refined0.171
r_nbtor_refined0.161
r_metal_ion_refined0.146
r_ncsr_local_group_10.093
r_symmetry_xyhbond_nbd_other0.088
r_symmetry_nbtor_other0.076
r_chiral_restr0.06
r_symmetry_xyhbond_nbd_refined0.057
r_bond_other_d0.034
r_gen_planes_other0.019
r_gen_planes_refined0.007
r_bond_refined_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9542
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms259

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing