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Cryptochrome B from Rhodobacter sphaeroides
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 0.3 M MGCL2, 0.1M BICINE PH 8.5, 29.5% PEG2000, 17.5% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 4.17 70.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.84 α = 90 b = 137.84 β = 90 c = 521.94 γ = 120
Symmetry Space Group P 65 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 CCD ADSC QUANTUM 315r TORODIAL FOCUSING MIRROR 2009-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.7 25 99.8 0.1 26.9 15.2 81535 -3 48.5
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 2.7 2.77 99.8 0.56 5.4 15.2
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 SAD THROUGHOUT NONE 2.7 24.95 79535 2000 100 0.19851 0.19774 0.1984 0.22837 0.2232 SHELLED 32.223
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] 1.63 0.82 1.63 -2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.948 r_dihedral_angle_4_deg 21.181 r_dihedral_angle_3_deg 17.039 r_dihedral_angle_1_deg 6.15 r_scangle_it 4.076 r_scbond_it 2.383 r_mcangle_it 1.586 r_angle_refined_deg 1.546 r_angle_other_deg 1.101 r_mcbond_it 0.793
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.948 r_dihedral_angle_4_deg 21.181 r_dihedral_angle_3_deg 17.039 r_dihedral_angle_1_deg 6.15 r_scangle_it 4.076 r_scbond_it 2.383 r_mcangle_it 1.586 r_angle_refined_deg 1.546 r_angle_other_deg 1.101 r_mcbond_it 0.793 r_mcbond_other 0.206 r_chiral_restr 0.088 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 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_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 11977 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 258
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHENIX phasing