☰ Navigation Tabs
Crystal structure of a mesophilic xylanase A from Bacillus subtilis 1A1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HV0 PDB entry 1HV0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 0.9M sodium tartrate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.9 34.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.931 α = 90 b = 70.499 β = 90 c = 42.044 γ = 90
Symmetry Space Group P 21 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 100 CCD MARRESEARCH 2004-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE D03B-MX1 1.427 LNLS D03B-MX1
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 1.7 41.9 0.092 7.2 1.9 14449
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) 1.7 1.76 81.3 0.269 2.5 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 PDB entry 1HV0 1.7 42.03 13705 744 83.78 0.17344 0.17138 0.1713 0.21163 0.2117 RANDOM 21.598
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] -1.98 0.94 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.847 r_dihedral_angle_4_deg 14.725 r_dihedral_angle_3_deg 11.958 r_dihedral_angle_1_deg 8.051 r_scangle_it 2.397 r_scbond_it 1.765 r_angle_refined_deg 1.586 r_mcangle_it 1.113 r_mcbond_it 0.678 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.847 r_dihedral_angle_4_deg 14.725 r_dihedral_angle_3_deg 11.958 r_dihedral_angle_1_deg 8.051 r_scangle_it 2.397 r_scbond_it 1.765 r_angle_refined_deg 1.586 r_mcangle_it 1.113 r_mcbond_it 0.678 r_nbtor_refined 0.32 r_symmetry_hbond_refined 0.247 r_nbd_refined 0.217 r_symmetry_vdw_refined 0.194 r_xyhbond_nbd_refined 0.163 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1447 Nucleic Acid Atoms Solvent Atoms 145 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement MAR345 data collection SCALEPACK data scaling AMoRE phasing