☰ Navigation Tabs
Crystal structure of the novel complex formed between Zinc 2-glycoprotein (ZAG) and Prolactin inducible protein (PIP) from human seminal plasma
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ZAG PDB ENTRY 1ZAG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 298 50mM sodium acetate, 20% PEG4000, pH6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.53 65.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.298 α = 90 b = 132.298 β = 90 c = 73.752 γ = 90
Symmetry Space Group P 4 21 2
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 MAR scanner 345 mm plate mirror 2006-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 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 3.2 25 98.8 0.139 7.4 10296 10296 36.71
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 3.2 3.25 0.523 2
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1ZAG 3.23 25 10296 10296 515 98.78 0.20033 0.1958 0.225 0.24041 0.2826 RANDOM 33.991
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] 0.36 0.36 -0.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.911 r_dihedral_angle_3_deg 19.027 r_dihedral_angle_4_deg 18.434 r_dihedral_angle_1_deg 5.83 r_angle_refined_deg 1.302 r_scangle_it 1.2 r_mcangle_it 0.787 r_scbond_it 0.663 r_mcbond_it 0.431 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.911 r_dihedral_angle_3_deg 19.027 r_dihedral_angle_4_deg 18.434 r_dihedral_angle_1_deg 5.83 r_angle_refined_deg 1.302 r_scangle_it 1.2 r_mcangle_it 0.787 r_scbond_it 0.663 r_mcbond_it 0.431 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.269 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.139 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3217 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 137
Software Software Software Name Purpose MAR345dtb data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling