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Crystal structure of the catalytic domain of XynA1 from Paenibacillus sp. JDR-2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 294.5 200mM HEPES, 100 mM MgCl2, 18% PEG3350, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 294.5K
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.072 α = 90 b = 93.172 β = 99.96 c = 182.947 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 105 CCD ADSC QUANTUM 315r Rh coated flat mirror. side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg 2008-08-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.980 SSRL BL7-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.34 179.61 602662
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.34 42.61 496837 26358 86.71 0.14421 0.14201 0.18546 0.2123 RANDOM 23.38
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] -0.49 0.32 -0.06 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.522 r_dihedral_angle_3_deg 12.555 r_dihedral_angle_4_deg 12.066 r_dihedral_angle_1_deg 7.602 r_scangle_it 6.673 r_scbond_it 4.873 r_mcangle_it 3.298 r_rigid_bond_restr 2.636 r_mcbond_it 2.425 r_angle_refined_deg 2.179
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.522 r_dihedral_angle_3_deg 12.555 r_dihedral_angle_4_deg 12.066 r_dihedral_angle_1_deg 7.602 r_scangle_it 6.673 r_scbond_it 4.873 r_mcangle_it 3.298 r_rigid_bond_restr 2.636 r_mcbond_it 2.425 r_angle_refined_deg 2.179 r_chiral_restr 0.166 r_bond_refined_d 0.027 r_gen_planes_refined 0.014 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 19224 Nucleic Acid Atoms Solvent Atoms 3312 Heterogen Atoms 20
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling