1N76 | pdb_00001n76

CRYSTAL STRUCTURE OF HUMAN SEMINAL LACTOFERRIN AT 3.4 A RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1B0LPDB ENTRY 1B0L

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS8298Tris-HCl, ethanol, pH 8.0, MICRODIALYSIS, temperature 298.0K
Crystal Properties
Matthews coefficientSolvent content
2.7255

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 56.052α = 90
b = 97.507β = 90
c = 156.79γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCHcrystal monochromator2001-10-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
13.42093.80.1596.421159411008-359.4
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)
13.43.52750.3271.9

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-Work (Depositor)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1B0L3.419.6511008110085541000.2320.219370.216950.26599RANDOM37.177
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]
3.91-1.76-2.15
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it8.69
r_dihedral_angle_1_deg6.776
r_scbond_it6.341
r_mcangle_it5.503
r_mcbond_it3.411
r_angle_other_deg2.126
r_angle_refined_deg2.061
r_symmetry_hbond_refined0.241
r_nbd_other0.22
r_nbd_refined0.207
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it8.69
r_dihedral_angle_1_deg6.776
r_scbond_it6.341
r_mcangle_it5.503
r_mcbond_it3.411
r_angle_other_deg2.126
r_angle_refined_deg2.061
r_symmetry_hbond_refined0.241
r_nbd_other0.22
r_nbd_refined0.207
r_symmetry_vdw_other0.197
r_xyhbond_nbd_refined0.177
r_symmetry_vdw_refined0.163
r_chiral_restr0.109
r_nbtor_other0.09
r_bond_refined_d0.035
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.005
r_dihedral_angle_2_deg
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5344
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms11

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement