5CRY

Structure of iron-saturated C-lobe of bovine lactoferrin at pH 6.8 indicates the softening of iron coordination


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4FJP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.83000.05M HEPES, 20% PEG 20K
Crystal Properties
Matthews coefficientSolvent content
3.5865.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 159.654α = 90
b = 82.58β = 128.08
c = 107.694γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300CCDMARRESEARCH2014-12-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.7939.4599.2164.12730727307

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4FJP2.7939.4525919136998.470.208690.205260.27287RANDOM67.421
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]
-0.270.18-3.151.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.205
r_dihedral_angle_4_deg21.866
r_dihedral_angle_3_deg20.049
r_long_range_B_refined10.158
r_long_range_B_other10.158
r_scangle_other7.626
r_mcangle_it7.446
r_mcangle_other7.445
r_dihedral_angle_1_deg7.389
r_scbond_it5.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.205
r_dihedral_angle_4_deg21.866
r_dihedral_angle_3_deg20.049
r_long_range_B_refined10.158
r_long_range_B_other10.158
r_scangle_other7.626
r_mcangle_it7.446
r_mcangle_other7.445
r_dihedral_angle_1_deg7.389
r_scbond_it5.065
r_scbond_other5.032
r_mcbond_it4.844
r_mcbond_other4.844
r_angle_other_deg3.681
r_angle_refined_deg1.852
r_chiral_restr0.106
r_gen_planes_other0.025
r_bond_refined_d0.018
r_gen_planes_refined0.012
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5316
Nucleic Acid Atoms
Solvent Atoms72
Heterogen Atoms155

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing