3IB2

structure of the complex of C-terminal half (C-lobe) of bovine lactoferrin with alpha-methyl-4-(2-methylpropyl) benzene acetic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.01M ZNSO4, 0.1M MES, 25% PEG, MONOMETHYL ETHER 550, PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.6753.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.319α = 90
b = 50.48β = 107.75
c = 66.116γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray300IMAGE PLATEMARRESEARCHMIRROR2007-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.2920890.1250.06415854
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)
12.292.3890.20.4771.9

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2DWA2.2920158411502781487.30.1680.1650.22RANDOM32.53
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]
-0.02-0.95-0.90.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.422
r_dihedral_angle_3_deg20.348
r_dihedral_angle_4_deg18.321
r_dihedral_angle_1_deg7.914
r_scangle_it5.175
r_scbond_it3.255
r_mcangle_it2.191
r_angle_refined_deg1.71
r_mcbond_it1.325
r_symmetry_hbond_refined0.654
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.422
r_dihedral_angle_3_deg20.348
r_dihedral_angle_4_deg18.321
r_dihedral_angle_1_deg7.914
r_scangle_it5.175
r_scbond_it3.255
r_mcangle_it2.191
r_angle_refined_deg1.71
r_mcbond_it1.325
r_symmetry_hbond_refined0.654
r_symmetry_metal_ion_refined0.457
r_symmetry_vdw_refined0.349
r_nbtor_refined0.314
r_nbd_refined0.238
r_xyhbond_nbd_refined0.176
r_chiral_restr0.136
r_metal_ion_refined0.135
r_bond_refined_d0.016
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2604
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms122

Software

Software
Software NamePurpose
DENZOdata reduction
AMoREphasing
REFMACrefinement
AUTOMARdata reduction
SCALEPACKdata scaling