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Beta-1,2-Mannobiose phosphorylase from Listeria innocua - glycerol complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 293 1.8 M (NH4)2SO4, 10 mM CoCl2, 0.1 M MES-NaOH
Crystal Properties Matthews coefficient Solvent content 4.01 69.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.559 α = 90 b = 146.559 β = 90 c = 106.324 γ = 120
Symmetry Space Group P 31 2 1
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 210 2013-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 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 1.9 50 100 0.057 50.1 9.4 103595
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 1.9 1.93 100 0.468 5.7 9.4
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 1VKD 1.9 34.14 98246 5168 99.82 0.16622 0.16458 0.177 0.19698 0.2077 RANDOM 30.598
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
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.598 r_dihedral_angle_4_deg 18.275 r_dihedral_angle_3_deg 12.026 r_long_range_B_refined 7.36 r_long_range_B_other 7.36 r_dihedral_angle_1_deg 7.205 r_scangle_other 5.878 r_scbond_it 4.228 r_scbond_other 4.228 r_mcangle_it 3.548
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.598 r_dihedral_angle_4_deg 18.275 r_dihedral_angle_3_deg 12.026 r_long_range_B_refined 7.36 r_long_range_B_other 7.36 r_dihedral_angle_1_deg 7.205 r_scangle_other 5.878 r_scbond_it 4.228 r_scbond_other 4.228 r_mcangle_it 3.548 r_mcangle_other 3.548 r_mcbond_it 3.02 r_mcbond_other 3.017 r_angle_refined_deg 2.205 r_angle_other_deg 1.112 r_chiral_restr 0.166 r_bond_refined_d 0.027 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5640 Nucleic Acid Atoms Solvent Atoms 701 Heterogen Atoms 107
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing