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Crystal structure of gp41-1 intein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KL5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.5 293 citric acid, magnesium sulfate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.12 41.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.809 α = 90 b = 69.986 β = 90 c = 71.236 γ = 90
Symmetry Space Group I 2 2 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 PIXEL DECTRIS PILATUS 6M-F 2014-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.02 49.92 92.1 0.038 0.019 31.5 4.2 57411
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 1.02 1.04
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 4KL5 1.02 49.92 53080 2642 89.35 0.12263 0.1212 0.1219 0.1498 0.1504 RANDOM 19.477
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] 0.08 0.11 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.897 r_dihedral_angle_3_deg 12.347 r_dihedral_angle_4_deg 8.366 r_dihedral_angle_1_deg 7.15 r_long_range_B_other 5.501 r_long_range_B_refined 5.5 r_rigid_bond_restr 5.075 r_scbond_it 4.011 r_scbond_other 4.008 r_scangle_other 3.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.897 r_dihedral_angle_3_deg 12.347 r_dihedral_angle_4_deg 8.366 r_dihedral_angle_1_deg 7.15 r_long_range_B_other 5.501 r_long_range_B_refined 5.5 r_rigid_bond_restr 5.075 r_scbond_it 4.011 r_scbond_other 4.008 r_scangle_other 3.543 r_angle_refined_deg 2.086 r_angle_other_deg 1.552 r_mcangle_it 1.195 r_mcangle_other 1.194 r_mcbond_it 0.984 r_mcbond_other 0.984 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.005 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_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1004 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing