☰ Navigation Tabs
Crystal structure of the PH domain of Evectin-2 from human complexed with O-phospho-L-serine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DHI PDB ENTRY 2DHI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 1.89 34.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.747 α = 90 b = 48.449 β = 92.2 c = 64.323 γ = 90
Symmetry Space Group P 1 21 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 210 2010-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1 100 97.1 0.054 46.8 6.3 102125
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 1 1.02 95.3 0.29 8.5 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2DHI 1 14.45 96954 5104 97.08 0.10606 0.10505 0.1074 0.12563 0.1282 RANDOM 7.642
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] -0.02 0.01 0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.642 r_dihedral_angle_4_deg 17.897 r_dihedral_angle_3_deg 13.127 r_dihedral_angle_1_deg 7.09 r_scangle_it 5.549 r_scbond_it 3.937 r_mcangle_it 2.77 r_angle_refined_deg 1.944 r_mcbond_it 1.799 r_rigid_bond_restr 1.486
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.642 r_dihedral_angle_4_deg 17.897 r_dihedral_angle_3_deg 13.127 r_dihedral_angle_1_deg 7.09 r_scangle_it 5.549 r_scbond_it 3.937 r_mcangle_it 2.77 r_angle_refined_deg 1.944 r_mcbond_it 1.799 r_rigid_bond_restr 1.486 r_angle_other_deg 1.012 r_mcbond_other 0.539 r_chiral_restr 0.126 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_gen_planes_other 0.003 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1824 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 23
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling