1SQY | pdb_00001sqy

Structure of human diferric lactoferrin at 2.5A resolution using crystals grown at pH 6.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B0L 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS6.5277Ethanol, Tris-HCL, pH 6.5, MICRODIALYSIS, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.754.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.156α = 90
b = 98.09β = 90
c = 157.036γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKUMIRROR2003-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5414

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
12.52096.80.0599.912.13676513046953.3
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)
12.52.56930.6022.5

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-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1B0L2.519.73304682892915391000.220.20440.203810.21517RANDOM48.154
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]
1.611.13-2.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.075
r_scangle_it3.742
r_dihedral_angle_1_deg2.304
r_scbond_it2.19
r_angle_refined_deg1.728
r_mcangle_it1.675
r_angle_other_deg1.125
r_mcbond_it0.884
r_nbtor_other0.472
r_nbd_refined0.256
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg19.075
r_scangle_it3.742
r_dihedral_angle_1_deg2.304
r_scbond_it2.19
r_angle_refined_deg1.728
r_mcangle_it1.675
r_angle_other_deg1.125
r_mcbond_it0.884
r_nbtor_other0.472
r_nbd_refined0.256
r_symmetry_vdw_refined0.243
r_nbd_other0.24
r_symmetry_vdw_other0.228
r_symmetry_hbond_refined0.198
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_other0.139
r_chiral_restr0.118
r_xyhbond_nbd_other0.108
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5347
Nucleic Acid Atoms
Solvent Atoms306
Heterogen Atoms66

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing