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E. coli (lacZ) beta-galactosidase (N460D) in complex with IPTG
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JYX PDB ENTRY 1JYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 288 10% PEG8000, 100 mM Bis-Tris, pH 6.5, 200 mM magnesium chloride, 100 mM sodium chloride, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.62 52.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.762 α = 90 b = 162.446 β = 90 c = 203.36 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 210 2006-09-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
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 2 204.12 93 0.069 10.5 3.5 312850 312850 19.2
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 2 2.11 67.1 0.371 2.5 1.9 32465
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1JYX 2 110.9 308138 308138 4492 100 0.17269 0.17269 0.17213 0.1752 0.21199 0.215 CONSISTENT WITH PREVIOUS STRUCTURES 25.369
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] 0.14 -0.27 0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.617 r_dihedral_angle_4_deg 14.432 r_dihedral_angle_3_deg 12.506 r_dihedral_angle_1_deg 6.065 r_scangle_it 6.033 r_scbond_it 4.295 r_mcangle_it 2.975 r_mcbond_it 2 r_angle_refined_deg 1.048 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.617 r_dihedral_angle_4_deg 14.432 r_dihedral_angle_3_deg 12.506 r_dihedral_angle_1_deg 6.065 r_scangle_it 6.033 r_scbond_it 4.295 r_mcangle_it 2.975 r_mcbond_it 2 r_angle_refined_deg 1.048 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32628 Nucleic Acid Atoms Solvent Atoms 3300 Heterogen Atoms 355
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection MOSFLM data reduction SCALA data scaling CNS phasing