3MJN

Crystal Structure of the complex of C-lobe of lactoferrin with isopropylamino-3-(1-naphthyloxy)propan-2-ol at 2.38 A Resolution


X-RAY DIFFRACTION

Starting Model(s)

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

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
2.6353.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.107α = 90
b = 50.248β = 107.82
c = 65.654γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300IMAGE PLATEMARRESEARCHMIRROR2010-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.541

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
12.3862.597.40.0949.11594315943
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)
2.382.4494.70.4481.9

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 REPLACEMENTTHROUGHOUT2DWA2.3862.5155191474677397.420.1760.174170.171480.21142RANDOM34.214
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]
0.32-1.33-0.6-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.053
r_dihedral_angle_4_deg19.539
r_dihedral_angle_3_deg17.331
r_dihedral_angle_1_deg6.63
r_scangle_it3.644
r_scbond_it2.1
r_mcangle_it1.516
r_angle_refined_deg1.428
r_mcbond_it0.844
r_symmetry_hbond_refined0.384
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.053
r_dihedral_angle_4_deg19.539
r_dihedral_angle_3_deg17.331
r_dihedral_angle_1_deg6.63
r_scangle_it3.644
r_scbond_it2.1
r_mcangle_it1.516
r_angle_refined_deg1.428
r_mcbond_it0.844
r_symmetry_hbond_refined0.384
r_nbtor_refined0.305
r_symmetry_vdw_refined0.303
r_nbd_refined0.212
r_xyhbond_nbd_refined0.133
r_symmetry_metal_ion_refined0.131
r_chiral_restr0.086
r_metal_ion_refined0.032
r_bond_refined_d0.011
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms238
Heterogen Atoms126

Software

Software
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling