☰ Navigation Tabs
Crystal structure of the hatching enzyme ZHE1 from the zebrafish Danio rerio
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1AST
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 0.1M MES-NaOH buffer, 20%(w/v) PEG 3350, 0.2M potassium sulphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.01 38.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.97 α = 90 b = 62.68 β = 90 c = 87.34 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 ADSC QUANTUM 210r 2009-06-02 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2008-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.00000 Photon Factory BL-5A 2 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00000 Photon Factory AR-NW12A
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 1.1 20 98.2 0.037 26.1 72995
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 1AST 1.1 14.98 69307 3688 98.23 0.16946 0.16852 0.1778 0.18722 0.1975 RANDOM 9.486
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] 1.59 -0.43 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.252 r_dihedral_angle_4_deg 22.267 r_dihedral_angle_3_deg 10.629 r_dihedral_angle_1_deg 5.914 r_scangle_it 4.561 r_scbond_it 3.084 r_mcangle_it 2.122 r_angle_refined_deg 1.498 r_mcbond_it 1.389 r_rigid_bond_restr 1.196
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.252 r_dihedral_angle_4_deg 22.267 r_dihedral_angle_3_deg 10.629 r_dihedral_angle_1_deg 5.914 r_scangle_it 4.561 r_scbond_it 3.084 r_mcangle_it 2.122 r_angle_refined_deg 1.498 r_mcbond_it 1.389 r_rigid_bond_restr 1.196 r_angle_other_deg 0.928 r_mcbond_other 0.452 r_chiral_restr 0.088 r_bond_refined_d 0.011 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1555 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 14
Software Software Software Name Purpose XDS data scaling MOLREP phasing REFMAC refinement XDS data reduction