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Time-Resolved Crystal Structure of HindIII with 60sec soaking
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A4K PDB ENTRY 3A4K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 10-15% PEG 3350, 300mM NaSCN, 10% v/v Glycerol, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.75 55.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.495 α = 90 b = 140.704 β = 112.07 c = 96.467 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 95 CCD ADSC QUANTUM 315r 2013-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.3 50 99.9 0.154 17 3.8 87848
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 2.3 2.34 100 0.915 2 3.8
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 3A4K 2.3 39.71 83386 4430 99.68 0.18423 0.18172 0.1879 0.23044 0.2318 RANDOM 40.958
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.115 r_dihedral_angle_3_deg 16.933 r_dihedral_angle_4_deg 16.019 r_dihedral_angle_1_deg 6.553 r_mcangle_it 4.635 r_scbond_it 4.213 r_mcbond_it 3.156 r_mcbond_other 3.153 r_angle_refined_deg 1.64 r_angle_other_deg 0.993
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.115 r_dihedral_angle_3_deg 16.933 r_dihedral_angle_4_deg 16.019 r_dihedral_angle_1_deg 6.553 r_mcangle_it 4.635 r_scbond_it 4.213 r_mcbond_it 3.156 r_mcbond_other 3.153 r_angle_refined_deg 1.64 r_angle_other_deg 0.993 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 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_mcangle_other r_scbond_other r_scangle_it 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 9808 Nucleic Acid Atoms 2920 Solvent Atoms 338 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing