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E. coli (lacZ) beta-galactosidase (N460T) in complex with galactonolactone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JZ5 PDB ENTRY 1JZ5
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 2.58 52.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.443 α = 90 b = 161.643 β = 90 c = 202.155 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 2.05 204.12 81.1 0.043 13 2.1 249661 249661 18.114
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 2.05 2.16 52.3 0.073 5.5 1.3 23130
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1JZ5 2.05 75.05 245685 245685 3564 100 0.15725 0.15725 0.15657 0.20532 0.2191 CONSISTENT WITH PREVIOUS STRUCTURES 26.514
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] -0.23 0.58 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_4_deg 14.157 r_dihedral_angle_3_deg 12.833 r_scangle_it 6.232 r_dihedral_angle_1_deg 6.115 r_scbond_it 4.587 r_mcangle_it 3.118 r_mcbond_it 2.181 r_angle_refined_deg 1.056 r_chiral_restr 0.072
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_4_deg 14.157 r_dihedral_angle_3_deg 12.833 r_scangle_it 6.232 r_dihedral_angle_1_deg 6.115 r_scbond_it 4.587 r_mcangle_it 3.118 r_mcbond_it 2.181 r_angle_refined_deg 1.056 r_chiral_restr 0.072 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 32624 Nucleic Acid Atoms Solvent Atoms 3458 Heterogen Atoms 379
Software Software Software Name Purpose REFMAC refinement CNS refinement ADSC data collection MOSFLM data reduction SCALA data scaling CNS phasing