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Crystal Structure Analysis of the clock protein EA4 (glycosylation form)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E9P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 27% PEG 3350, 500mM magnesium chloride, 20mM sodium fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.41 48.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.098 α = 90 b = 73.894 β = 104.07 c = 47.446 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 2005-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 20 95.5 4.1 17500
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 2.1 2.18 4.1 17500
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 1E9P 2.11 20 16602 878 95.29 0.17425 0.17019 0.1778 0.2511 0.2546 RANDOM 32.62
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] -1.58 -3.3 -1.45 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.756 r_dihedral_angle_4_deg 18.57 r_dihedral_angle_3_deg 18.015 r_dihedral_angle_1_deg 6.773 r_scangle_it 5.813 r_scbond_it 4.443 r_mcangle_it 2.388 r_angle_refined_deg 2.066 r_mcbond_it 1.468 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.756 r_dihedral_angle_4_deg 18.57 r_dihedral_angle_3_deg 18.015 r_dihedral_angle_1_deg 6.773 r_scangle_it 5.813 r_scbond_it 4.443 r_mcangle_it 2.388 r_angle_refined_deg 2.066 r_mcbond_it 1.468 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.292 r_nbd_refined 0.227 r_xyhbond_nbd_refined 0.195 r_symmetry_hbond_refined 0.186 r_chiral_restr 0.159 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2299 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing