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Protein crystal structure of xylanase A1 of Paenibacillus sp. JDR-2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 294.5 Protein to mother liquor at 2:1 ratio. mother liquor, 18% PEG 3350, 100mM HEPES, 200mM MgCl2, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 294.5K
Crystal Properties Matthews coefficient Solvent content 2.94 58.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 165.113 α = 90 b = 165.113 β = 90 c = 66.355 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD MARMOSAIC 325 mm CCD 2009-02-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.979 SSRL BL12-2
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 1.49 117.04 0.047 33.7 8.8 149014 148538
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-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 1.49 117.04 140983 7447 99.67 0.1472 0.14523 0.1455 0.18415 0.1851 RANDOM 30.787
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] 0.75 0.75 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.002 r_dihedral_angle_3_deg 13.92 r_dihedral_angle_4_deg 12.646 r_scangle_it 7.428 r_dihedral_angle_1_deg 6.963 r_scbond_it 5.479 r_mcangle_it 3.612 r_rigid_bond_restr 3.164 r_mcbond_it 2.652 r_angle_refined_deg 2.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.002 r_dihedral_angle_3_deg 13.92 r_dihedral_angle_4_deg 12.646 r_scangle_it 7.428 r_dihedral_angle_1_deg 6.963 r_scbond_it 5.479 r_mcangle_it 3.612 r_rigid_bond_restr 3.164 r_mcbond_it 2.652 r_angle_refined_deg 2.321 r_chiral_restr 0.188 r_bond_refined_d 0.029 r_gen_planes_refined 0.013 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5300 Nucleic Acid Atoms Solvent Atoms 720 Heterogen Atoms 140
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement HKL-2000 data scaling