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beta-galactosidase from Arthrobacter sp. C2-2 (isoenzyme C2-2-1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DP0 PDB ENTRY 1DP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 PEG 4000, sodium chloride, amonium sulphate, sodium citrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.62 68.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140.091 α = 90 b = 205.698 β = 102.34 c = 140.458 γ = 90
Symmetry Space Group P 1 21 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 2003-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9168 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 40 95 0.085 10.3 2.6 607777 577572 -5 17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.93 81 0.451 2.1 1.9 24388
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DP0 1.9 40 607830 577466 5775 95.02 0.15702 0.15702 0.15701 0.1574 0.195 0.167 RANDOM 18.018
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] -0.16 -0.35 0.64 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.663 r_dihedral_angle_4_deg 17.565 r_dihedral_angle_3_deg 13.463 r_dihedral_angle_1_deg 6.298 r_scangle_it 3.514 r_scbond_it 2.206 r_angle_refined_deg 1.472 r_mcangle_it 1.399 r_mcbond_it 0.78 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.663 r_dihedral_angle_4_deg 17.565 r_dihedral_angle_3_deg 13.463 r_dihedral_angle_1_deg 6.298 r_scangle_it 3.514 r_scbond_it 2.206 r_angle_refined_deg 1.472 r_mcangle_it 1.399 r_mcbond_it 0.78 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.228 r_nbd_refined 0.193 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.141 r_metal_ion_refined 0.116 r_chiral_restr 0.105 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 47305 Nucleic Acid Atoms Solvent Atoms 6513 Heterogen Atoms 79
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling AMoRE phasing REFMAC refinement