3O97

Crystal Structure of the complex of C-lobe of lactoferrin with indole acetic acid at 2.68 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IB1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52980.01M Znso4, 0.1M MES, 25% PEG, Monomethyl Ether 550, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6653.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.234α = 90
b = 50.396β = 107.7
c = 65.893γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300IMAGE PLATEMARRESEARCHMIRROR2010-07-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.541

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
12.6863.2598.29.81126610731
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.682.7899.8

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3IB12.6863.24103091030953599.590.1760.174560.172140.22243RANDOM39.988
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]
0.91-1.33-1.44-0.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.795
r_dihedral_angle_3_deg17.971
r_dihedral_angle_4_deg16.086
r_dihedral_angle_1_deg6.097
r_scangle_it3.793
r_scbond_it2.296
r_angle_refined_deg2.075
r_mcangle_it1.715
r_mcbond_it0.963
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.795
r_dihedral_angle_3_deg17.971
r_dihedral_angle_4_deg16.086
r_dihedral_angle_1_deg6.097
r_scangle_it3.793
r_scbond_it2.296
r_angle_refined_deg2.075
r_mcangle_it1.715
r_mcbond_it0.963
r_nbtor_refined0.308
r_symmetry_hbond_refined0.307
r_symmetry_vdw_refined0.285
r_nbd_refined0.237
r_xyhbond_nbd_refined0.161
r_metal_ion_refined0.128
r_chiral_restr0.092
r_symmetry_metal_ion_refined0.06
r_bond_refined_d0.02
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms95

Software

Software
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling