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CRYSTAL STRUCTURE OF HUMAN SEMINAL LACTOFERRIN AT 3.4 A RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B0L PDB ENTRY 1B0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 8 298 Tris-HCl, ethanol, pH 8.0, MICRODIALYSIS, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.72 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.052 α = 90 b = 97.507 β = 90 c = 156.79 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 IMAGE PLATE MARRESEARCH crystal monochromator 2001-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.4 20 93.8 0.159 6.4 2 11594 11008 -3 59.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.4 3.52 75 0.327 1.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (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 Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1B0L 3.4 19.65 11008 11008 554 100 0.232 0.21937 0.21695 0.26599 RANDOM 37.177
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 Key Refinement Restraint Deviation r_scangle_it 8.69 r_dihedral_angle_1_deg 6.776 r_scbond_it 6.341 r_mcangle_it 5.503 r_mcbond_it 3.411 r_angle_other_deg 2.126 r_angle_refined_deg 2.061 r_symmetry_hbond_refined 0.241 r_nbd_other 0.22 r_nbd_refined 0.207
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 8.69 r_dihedral_angle_1_deg 6.776 r_scbond_it 6.341 r_mcangle_it 5.503 r_mcbond_it 3.411 r_angle_other_deg 2.126 r_angle_refined_deg 2.061 r_symmetry_hbond_refined 0.241 r_nbd_other 0.22 r_nbd_refined 0.207 r_symmetry_vdw_other 0.197 r_xyhbond_nbd_refined 0.177 r_symmetry_vdw_refined 0.163 r_chiral_restr 0.109 r_nbtor_other 0.09 r_bond_refined_d 0.035 r_gen_planes_refined 0.008 r_bond_other_d 0.006 r_gen_planes_other 0.005 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 Atoms Number Protein Atoms 5344 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement