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Interaction of VHR with SA3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VHR PDB ENTRY 1VHR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 297 100 mM Tris 15% polyethylene glycol 8000, 60 mM NaF, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K
Crystal Properties Matthews coefficient Solvent content 2.21 44.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.406 α = 90 b = 59.186 β = 98.36 c = 60.656 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 140 IMAGE PLATE RIGAKU RAXIS IV 2006-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 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 1.9 50 99.1 0.059 6.8 2657 26330 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.95 99.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1VHR 1.9 50 1 26569 26330 1408 99.08 0.18046 0.17841 0.1786 0.21901 0.2182 RANDOM 15.51
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] 0.79 -0.58 -0.49 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.973 r_dihedral_angle_4_deg 17.852 r_dihedral_angle_3_deg 15.395 r_dihedral_angle_1_deg 9.92 r_scangle_it 4.051 r_scbond_it 2.541 r_angle_refined_deg 1.724 r_mcangle_it 1.464 r_mcbond_it 0.912 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.973 r_dihedral_angle_4_deg 17.852 r_dihedral_angle_3_deg 15.395 r_dihedral_angle_1_deg 9.92 r_scangle_it 4.051 r_scbond_it 2.541 r_angle_refined_deg 1.724 r_mcangle_it 1.464 r_mcbond_it 0.912 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.273 r_chiral_restr 0.247 r_nbd_refined 0.223 r_symmetry_vdw_refined 0.213 r_xyhbond_nbd_refined 0.153 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 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 2784 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 28
Software Software Software Name Purpose HKL-2000 data collection CCP4 model building REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CCP4 phasing