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Structure of cryptochrome 3 - DNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2J4D PDB ENTRY 2J4D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 10 MG/ML PROTEIN, 85 MM NA-CITRATE PH 4.6, 170 MM NH4-ACETATE, 21.5% (W/V) PEG 4000 AND 15% (V/V) GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.36 47.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.734 α = 90 b = 136.082 β = 90 c = 211.484 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH MIRRORS 2007-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7A EMBL/DESY, HAMBURG BW7A
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 15.1 99.2 0.1 14.9 6.02 229217 -3
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 2.05 89.6 0.41 2.8
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 2J4D 2.01 15.03 227588 1518 99.2 0.185 0.184 0.1949 0.222 0.2311 RANDOM 35.98
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 -0.02 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.206 r_dihedral_angle_4_deg 18.282 r_dihedral_angle_3_deg 12.852 r_dihedral_angle_1_deg 5.451 r_scangle_it 1.622 r_angle_refined_deg 1.151 r_scbond_it 1.014 r_angle_other_deg 0.867 r_mcangle_it 0.8 r_mcbond_it 0.471
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.206 r_dihedral_angle_4_deg 18.282 r_dihedral_angle_3_deg 12.852 r_dihedral_angle_1_deg 5.451 r_scangle_it 1.622 r_angle_refined_deg 1.151 r_scbond_it 1.014 r_angle_other_deg 0.867 r_mcangle_it 0.8 r_mcbond_it 0.471 r_symmetry_vdw_refined 0.246 r_symmetry_vdw_other 0.217 r_nbd_refined 0.197 r_nbd_other 0.183 r_nbtor_refined 0.18 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.131 r_nbtor_other 0.079 r_chiral_restr 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 23956 Nucleic Acid Atoms 520 Solvent Atoms 1305 Heterogen Atoms 528
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing