7EQU

Crystal structure of the C-lobe of lactoferrin produced by limited proteolysis using pepsin at 2.74A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5HBC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298Magnesium acetate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
3.5265.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 153.759α = 90
b = 81.554β = 129.949
c = 111.364γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2021-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID30B0.9655ESRFID30B

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.7476.8597.50.060.070.9910.22.927187
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.742.790.030.040.99

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 REPLACEMENTNONE5HBC2.74376.84627050136196.9950.2420.23880.298470
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]
2.5352.636-13.12.559
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.207
r_dihedral_angle_4_deg22.618
r_dihedral_angle_3_deg21.628
r_lrange_it15.116
r_lrange_other15.114
r_mcangle_it11.547
r_mcangle_other11.545
r_scangle_it11.027
r_scangle_other11.026
r_mcbond_it7.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.207
r_dihedral_angle_4_deg22.618
r_dihedral_angle_3_deg21.628
r_lrange_it15.116
r_lrange_other15.114
r_mcangle_it11.547
r_mcangle_other11.545
r_scangle_it11.027
r_scangle_other11.026
r_mcbond_it7.75
r_mcbond_other7.749
r_scbond_it7.218
r_scbond_other7.218
r_dihedral_angle_1_deg6.843
r_angle_refined_deg1.681
r_angle_other_deg1.199
r_nbd_other0.299
r_symmetry_nbd_refined0.253
r_nbd_refined0.214
r_symmetry_nbd_other0.21
r_symmetry_xyhbond_nbd_refined0.202
r_xyhbond_nbd_refined0.187
r_nbtor_refined0.163
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.062
r_chiral_restr0.056
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.005
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5316
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms221

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing