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Crystal structure of the catalytic domain of beta-amylase from paenibacillus polymyxa
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5BCA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2M AMMONIUM SULFATE, 0.1M TRIS, 25% PEG 6000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.14 42.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.028 α = 90 b = 68.519 β = 90 c = 93.904 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 95 CCD ADSC QUANTUM 315r 2011-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
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 1.94 50 19 0.096 29.5 7.1 29853 29847
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 1.94 1.97 100 0.444 5.8 7.1
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 (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 5BCA 1.95 41 29853 27870 1487 99.71 0.15499 0.15315 0.1547 0.19021 0.1933 RANDOM 19.729
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.59 r_dihedral_angle_4_deg 19.606 r_dihedral_angle_3_deg 12.594 r_dihedral_angle_1_deg 5.577 r_scangle_it 2.897 r_scbond_it 1.824 r_angle_refined_deg 1.163 r_mcangle_it 1.053 r_mcbond_it 0.548 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.59 r_dihedral_angle_4_deg 19.606 r_dihedral_angle_3_deg 12.594 r_dihedral_angle_1_deg 5.577 r_scangle_it 2.897 r_scbond_it 1.824 r_angle_refined_deg 1.163 r_mcangle_it 1.053 r_mcbond_it 0.548 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3216 Nucleic Acid Atoms Solvent Atoms 282 Heterogen Atoms 55
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling