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Lutheran glycoprotein, N-terminal domains 1 and 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PET PDB ENTRY 2PET
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 18% PEG4000, 0.2M ammonium acetate, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.97 37.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.248 α = 90 b = 52.248 β = 90 c = 256.842 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2006-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.1 1.488 SRS PX14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 100 90.1 0.102 10 5.6 19830 19830 -3 -3 45.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 41.3 0.482 1.2 1.8 891
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2PET 2.2 85.75 19755 19755 1014 90.11 0.207 0.207 0.205 0.2048 0.251 0.2463 RANDOM 43.696
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] 1.2 0.6 1.2 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.585 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 14.558 r_dihedral_angle_1_deg 4.801 r_scangle_it 3.884 r_scbond_it 2.582 r_mcangle_it 1.561 r_angle_refined_deg 1.498 r_mcbond_it 1.237 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.585 r_dihedral_angle_4_deg 18.113 r_dihedral_angle_3_deg 14.558 r_dihedral_angle_1_deg 4.801 r_scangle_it 3.884 r_scbond_it 2.582 r_mcangle_it 1.561 r_angle_refined_deg 1.498 r_mcbond_it 1.237 r_nbtor_refined 0.306 r_nbd_refined 0.219 r_symmetry_hbond_refined 0.207 r_symmetry_vdw_refined 0.198 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.085 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3592 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling