1NKX

CRYSTAL STRUCTURE OF A PROTEOLYTICALLY GENERATED FUNCTIONAL MONOFERRIC C-LOBE OF BOVINE LACTOFERRIN AT 1.9A RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BLFPDB ENTRY 1BLF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.52980.1M MES, 25% POLYETHYLENE GLYCOL MONOMETHYL ETHER 550 AND 0.01 M ZINC SULPHATE, pH 6.5, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.359α = 90
b = 50.471β = 107.72
c = 65.934γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray283IMAGE PLATEMARRESEARCHmirrors2002-07-12MSINGLE 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
11.920970.0570.05717.5629084-3-325.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.92840.230.233.642482

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1BLF1.9202820528205138296.80.2020.2020.1920.222RANDOM34.4
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]
3.92-5.09-1.85-2.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg22.4
r_scangle_it3.67
r_mcangle_it2.43
r_scbond_it2.3
r_mcbond_it1.48
r_angle_refined_deg1.3
r_improper_angle_d0.76
r_bond_refined_d0.005
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg22.4
r_scangle_it3.67
r_mcangle_it2.43
r_scbond_it2.3
r_mcbond_it1.48
r_angle_refined_deg1.3
r_improper_angle_d0.76
r_bond_refined_d0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_chiral_restr
r_gen_planes_refined
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2593
Nucleic Acid Atoms
Solvent Atoms226
Heterogen Atoms132

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing