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Crystal Structure of the PHR domain of Cryptochrome 1 from Arabidopsis thaliana with AMPPNP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DNP E.coli photolyase (PDB entry 1DNP)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 303 glycerol, MES, sulfobetaine-195, 1,6-hexanediol, sodium, potassium tartrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 3.7 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.213 α = 90 b = 169.213 β = 90 c = 104.521 γ = 120
Symmetry Space Group P 63 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 CUSTOM-MADE 2004-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.999 APS 19-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 2.45 50 98.3 0.059 37.6 11.4 32456 32456 -3 38.2
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) 2.45 2.54 91.4 0.583 3 10.8 2955
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 E.coli photolyase (PDB entry 1DNP) 2.45 50 30708 30708 3043 93.4 0.21 0.204 0.204 0.2051 0.253 0.2541 RANDOM 52.3
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] 8.03 11.61 8.03 -16.06
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23.2 c_scangle_it 7.32 c_scbond_it 5.64 c_mcangle_it 4.73 c_mcbond_it 3.42 c_angle_deg 1.9 c_improper_angle_d 1.25 c_bond_d 0.015
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3941 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 101
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing