☰ Navigation Tabs
ArfGap domain of HIV-1 Rev binding protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IQJ PDB entry 2IQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 2.27M Ammonium phosphate, 0.09M BTP, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.3 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.883 α = 90 b = 57.883 β = 90 c = 83.696 γ = 90
Symmetry Space Group P 43 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 100 CCD ADSC QUANTUM 4 2006-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1.00000 APS 17-ID
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 1.48 50 99.7 0.055 18.9 7.2 45446
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 1.48 1.53 97.3 0.237 4.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE-R PDB entry 2IQJ 1.48 30 24481 1239 99.825 0.18 0.1797 0.2095 0.1948 0.2148 random 12.863
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] 0.172 0.172 -0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.201 r_dihedral_angle_4_deg 17.554 r_dihedral_angle_3_deg 10.657 r_dihedral_angle_1_deg 5.842 r_scangle_it 4.116 r_scbond_it 2.835 r_mcangle_it 2.683 r_mcbond_it 2.268 r_angle_refined_deg 1.459 r_angle_other_deg 0.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.201 r_dihedral_angle_4_deg 17.554 r_dihedral_angle_3_deg 10.657 r_dihedral_angle_1_deg 5.842 r_scangle_it 4.116 r_scbond_it 2.835 r_mcangle_it 2.683 r_mcbond_it 2.268 r_angle_refined_deg 1.459 r_angle_other_deg 0.922 r_mcbond_other 0.495 r_symmetry_vdw_other 0.251 r_nbd_refined 0.212 r_nbd_other 0.201 r_nbtor_refined 0.179 r_symmetry_vdw_refined 0.133 r_xyhbond_nbd_refined 0.113 r_chiral_restr 0.095 r_symmetry_hbond_refined 0.093 r_nbtor_other 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1056 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 33
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection