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Zg3597, a family 117 glycoside hydrolase, produced by the marine bacterium Zobellia galactanivorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3P2N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 The optimized crystallization conditions for Zg3597 were: 16% glycerol, 0.15 M ammonium sulfate, and 20 % PEG 4000 in a 1:1 ratio with protein at 5 and 2.5 mg/mL and 14% PEG 3350 and 75 mM sodium acetate with a ratio of 2:1 protein (at 7.5 mg/mL) to mother liquor.
Crystal Properties Matthews coefficient Solvent content 3.03 59.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 187.79 α = 90 b = 223.52 β = 90 c = 225.22 γ = 90
Symmetry Space Group F 2 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 2012-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.979 ESRF ID14-4
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 2.3 30 99.7 13.2 6 103865
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 2.3 2.42
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 3P2N 2.3 30 98705 5189 99.68 0.18016 0.1778 0.1776 0.22521 0.2246 RANDOM 38.537
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] -1.66 1.24 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.665 r_dihedral_angle_4_deg 19.325 r_dihedral_angle_3_deg 17.178 r_long_range_B_refined 9.322 r_dihedral_angle_1_deg 7.569 r_mcangle_it 5.806 r_scbond_it 4.539 r_mcbond_it 3.801 r_angle_refined_deg 1.885 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.665 r_dihedral_angle_4_deg 19.325 r_dihedral_angle_3_deg 17.178 r_long_range_B_refined 9.322 r_dihedral_angle_1_deg 7.569 r_mcangle_it 5.806 r_scbond_it 4.539 r_mcbond_it 3.801 r_angle_refined_deg 1.885 r_chiral_restr 0.136 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other 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 10693 Nucleic Acid Atoms Solvent Atoms 701 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing