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Catalytic domain of beta-agarase from Microbulbifer thermotolerans JAMB-A94
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ATF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 283 1M trisodium citrate, 0.3M ammonium nitrtate, 3% ethanol, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.43 49.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.624 α = 90 b = 69.394 β = 90 c = 90.367 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 2012-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 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 1.6 50 100 0.031 59.5 7.2 41972
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 1.6 1.66 100 0.124 18.3 7.1
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 4ATF 1.6 37.86 39772 2117 99.93 0.15256 0.15191 0.165 0.16463 0.1731 RANDOM 12.759
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.976 r_dihedral_angle_4_deg 15.23 r_dihedral_angle_3_deg 11.25 r_dihedral_angle_1_deg 7.672 r_long_range_B_refined 3.687 r_angle_other_deg 3.63 r_long_range_B_other 3.318 r_scangle_other 1.6 r_angle_refined_deg 1.462 r_mcangle_it 1.191
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.976 r_dihedral_angle_4_deg 15.23 r_dihedral_angle_3_deg 11.25 r_dihedral_angle_1_deg 7.672 r_long_range_B_refined 3.687 r_angle_other_deg 3.63 r_long_range_B_other 3.318 r_scangle_other 1.6 r_angle_refined_deg 1.462 r_mcangle_it 1.191 r_mcangle_other 1.19 r_scbond_it 1.04 r_scbond_other 1.038 r_mcbond_it 0.722 r_mcbond_other 0.717 r_chiral_restr 0.084 r_gen_planes_other 0.011 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2236 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 14
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling