☰ Navigation Tabs
Crystal structure of PDF from the Vibrio parahaemolyticus bacteriophage VP16T - crystal form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LRY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 292 28% PEG-1000
100mM sodium acetate
Crystal Properties Matthews coefficient Solvent content 2.53 51.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.26 α = 90 b = 64.26 β = 90 c = 125.69 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 PIXEL DECTRIS PILATUS 6M 2013-07-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.980110 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) CC (Half) 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 1.5 50 99.7 0.04 0.999 17.35 4.32 48767 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 100 0.581 0.778 4.36
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 1LRY 1.5 41.67 46328 2439 100 0.18782 0.18668 0.184 0.20957 0.2061 RANDOM 22.342
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] 0.11 0.05 0.11 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.091 r_dihedral_angle_4_deg 17.631 r_dihedral_angle_3_deg 12.274 r_dihedral_angle_1_deg 5.344 r_scangle_it 2.987 r_scbond_it 2.032 r_angle_refined_deg 1.311 r_mcangle_it 1.182 r_mcbond_it 0.782 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.091 r_dihedral_angle_4_deg 17.631 r_dihedral_angle_3_deg 12.274 r_dihedral_angle_1_deg 5.344 r_scangle_it 2.987 r_scbond_it 2.032 r_angle_refined_deg 1.311 r_mcangle_it 1.182 r_mcbond_it 0.782 r_nbtor_refined 0.302 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.137 r_metal_ion_refined 0.091 r_chiral_restr 0.087 r_symmetry_hbond_refined 0.062 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2049 Nucleic Acid Atoms Solvent Atoms 329 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing