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High resolution structure of Penicillium chrysogenum alpha-L-arabinanase complexed with arabinobiose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A71 PDB ENTRY 3A71
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 277 28% MPD, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 2.61 52.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.959 α = 90 b = 77.117 β = 90 c = 79.574 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 2006-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 1.04 10 99.6 0.053 26.5 7 196659 9.3
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 1.04 1.08 98 0.363 2.3 6.3
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB ENTRY 3A71 1.04 10 186439 186439 9813 94.7 0.1044 0.1254 0.1172 RANDOM 6.94
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 2652 3340
RMS Deviations Key Refinement Restraint Deviation s_anti_bump_dis_restr 0.155 s_approx_iso_adps 0.108 s_zero_chiral_vol 0.099 s_non_zero_chiral_vol 0.092 s_similar_adp_cmpnt 0.035 s_from_restr_planes 0.0343 s_angle_d 0.03 s_bond_d 0.017 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2771 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 19
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing SHELXL-97 refinement