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Crystal structure of the Caf1A usher protein N-terminal domain from Yersinia pestis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other INTERNAL STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.3 293 SITTING DROPS 1 MKL OF CAF1AN 6 MG/ML PLUS 1 MKL OF 20% PEG 3350, 0.2 M AMMONIUM NITRATE, PH 6.3 AT 20 DEG C, 2-6 MONTHS
Crystal Properties Matthews coefficient Solvent content 1.9 36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.858 α = 90 b = 68.587 β = 90 c = 192.245 γ = 90
Symmetry Space Group C 2 2 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 CCD 2006-07-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2 29.5 97 0.08 16 4.9 27484 35.4
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 2 2.07 87 0.32 3 2.2
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 INTERNAL STRUCTURE 2 30 27313 1365 97.22 0.20487 0.20524 0.2061 0.26135 0.2159 RANDOM 37.63
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] -0.13 -0.03 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.121 r_dihedral_angle_4_deg 21.487 r_dihedral_angle_3_deg 16.644 r_dihedral_angle_1_deg 5.921 r_scangle_it 3.819 r_scbond_it 2.483 r_mcangle_it 1.619 r_angle_refined_deg 1.594 r_angle_other_deg 1.552 r_mcbond_it 0.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.121 r_dihedral_angle_4_deg 21.487 r_dihedral_angle_3_deg 16.644 r_dihedral_angle_1_deg 5.921 r_scangle_it 3.819 r_scbond_it 2.483 r_mcangle_it 1.619 r_angle_refined_deg 1.594 r_angle_other_deg 1.552 r_mcbond_it 0.959 r_mcbond_other 0.253 r_symmetry_vdw_other 0.235 r_nbd_refined 0.196 r_nbd_other 0.192 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_refined 0.152 r_symmetry_hbond_refined 0.115 r_chiral_restr 0.098 r_nbtor_other 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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_mcangle_other r_scbond_other 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 3069 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing