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Ab initio phasing of a nucleoside hydrolase-related hypothetical protein from Saccharophagus degradans that is associated with carbohydrate metabolism
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.2 M NACL, 0.1 M BIS-TRIS, PH 5.5, 25% POLYETHYLENE GLYCOL 3350.
Crystal Properties Matthews coefficient Solvent content 2.34 47.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.58 α = 90 b = 61.58 β = 90 c = 125.46 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 113 CCD MARRESEARCH M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.08 40 96.2 0.06 17.3 9 173965 2 12.4
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 1.08 1.14 82.9 0.39 3.8 5.8
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 DIRECT METHODS THROUGHOUT NONE 1.08 62.73 165083 8709 95.9 0.13403 0.13312 0.1453 0.15132 0.1621 RANDOM 8.801
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] 0.46 -0.17 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.467 r_dihedral_angle_4_deg 20.354 r_dihedral_angle_3_deg 10.168 r_dihedral_angle_1_deg 7.202 r_scangle_it 5.075 r_scbond_it 4.139 r_rigid_bond_restr 2.742 r_mcangle_it 2.595 r_mcbond_it 1.895 r_angle_refined_deg 1.526
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.467 r_dihedral_angle_4_deg 20.354 r_dihedral_angle_3_deg 10.168 r_dihedral_angle_1_deg 7.202 r_scangle_it 5.075 r_scbond_it 4.139 r_rigid_bond_restr 2.742 r_mcangle_it 2.595 r_mcbond_it 1.895 r_angle_refined_deg 1.526 r_angle_other_deg 0.897 r_mcbond_other 0.755 r_chiral_restr 0.111 r_gen_planes_refined 0.014 r_bond_refined_d 0.012 r_gen_planes_other 0.002 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3140 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling ACORN phasing