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Crystal structure of chitinase-like agglutinin RobpsCRA from Robinia pseudoacacia
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NWU MODEL GENERATED BY PHYRE SERVER BASED ON PDB ENTRY 1NWU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 35,8% (V/V) MPD, 0.1 M NA/K2 PHOSPHATE PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.05 40
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.1 α = 106.01 b = 53.221 β = 94.12 c = 71.271 γ = 107.59
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 MAR25 2009-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.85 67 97.3 0.07 15.5 4.3 47466 19.4
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 1.85 1.95 96.1 0.42 3.5 3.5
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 MODEL GENERATED BY PHYRE SERVER BASED ON PDB ENTRY 1NWU 1.85 34.48 45067 2398 97.18 0.15038 0.14838 0.158 0.18731 0.1947 RANDOM 22.891
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] -0.08 -0.89 -0.38 -1.86 1.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.884 r_dihedral_angle_4_deg 19.479 r_dihedral_angle_3_deg 12.783 r_dihedral_angle_1_deg 6.124 r_angle_refined_deg 1.421 r_angle_other_deg 0.813 r_symmetry_vdw_refined 0.351 r_symmetry_vdw_other 0.277 r_nbd_refined 0.247 r_symmetry_hbond_refined 0.237
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.884 r_dihedral_angle_4_deg 19.479 r_dihedral_angle_3_deg 12.783 r_dihedral_angle_1_deg 6.124 r_angle_refined_deg 1.421 r_angle_other_deg 0.813 r_symmetry_vdw_refined 0.351 r_symmetry_vdw_other 0.277 r_nbd_refined 0.247 r_symmetry_hbond_refined 0.237 r_nbtor_refined 0.187 r_nbd_other 0.174 r_xyhbond_nbd_refined 0.155 r_chiral_restr 0.09 r_nbtor_other 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5210 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing