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The 1.26 angstrom resolution structure of Bacillus cereus beta-amylase in complex with maltose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1B9Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 HANGING DROP VAPOR DIFFUSION AGAINST 0.1 M PHOSPHATE BUFFER PH 6.5, 15% PEG 6000 AND 5% SATN. AMMONIUM SULFATE WITH A PROTEIN CONCENTRATION OF 15MG/ML.
Crystal Properties Matthews coefficient Solvent content 2.82 56.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.974 α = 90 b = 89.843 β = 103.09 c = 66.035 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 4r 2002-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0000 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 1.26 50 99.3 0.047 0.054 0.995 48.5 3.3 171593 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.26 1.28 80.5 0.182 0.246 0.946 5.95 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (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 FREE R-VALUE 1.26 10 162442 8573 93.4 0.124 0.1215 0.1645 0.1581 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 69 5150.4
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.38 s_approx_iso_adps 0.1605 s_similar_adp_cmpnt 0.0481 s_anti_bump_dis_restr 0.0472 s_angle_d 0.0318 s_bond_d 0.0143 s_from_restr_planes 0.006 s_similar_dist s_zero_chiral_vol s_rigid_bond_adp_cmpnt
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4371 Nucleic Acid Atoms Solvent Atoms 887 Heterogen Atoms 222
Software Software Software Name Purpose PHENIX phasing SHELXL-97 refinement HKL-2000 data reduction HKL-2000 data scaling