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Structure of AAP A domain and B-repeats (residues 351-813) from Staphylococcus epidermidis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7SIE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 20% PEG 550 MME, 10% PEG 20K, 100 mM MOPS/HEPES pH 7 (Morpheus Buffer System 2)
Crystal Properties Matthews coefficient Solvent content 2.54 51.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.482 α = 84.695 b = 66.565 β = 80.489 c = 66.873 γ = 89.664
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9795 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.3 39.709 97.5 0.08 0.113 0.08 0.989 4.8 2.2 42896
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 96.9 0.586 0.829 0.586 0.764 1.3 2.1
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 (All) 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 7SIE 2.3 39.709 42895 2120 97.517 0.2 0.1975 0.2027 0.2426 0.2439 RANDOM 51.537
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] -3.365 0.378 0.289 -2.534 -1.177 5.386
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.408 r_dihedral_angle_3_deg 15.058 r_dihedral_angle_2_deg 8.264 r_dihedral_angle_1_deg 7.534 r_lrange_it 6.829 r_lrange_other 6.829 r_scangle_it 3.649 r_scangle_other 3.649 r_mcangle_it 3.589 r_mcangle_other 3.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.408 r_dihedral_angle_3_deg 15.058 r_dihedral_angle_2_deg 8.264 r_dihedral_angle_1_deg 7.534 r_lrange_it 6.829 r_lrange_other 6.829 r_scangle_it 3.649 r_scangle_other 3.649 r_mcangle_it 3.589 r_mcangle_other 3.589 r_scbond_it 2.384 r_scbond_other 2.384 r_mcbond_it 2.266 r_mcbond_other 2.266 r_angle_refined_deg 1.407 r_angle_other_deg 0.492 r_metal_ion_refined 0.2 r_symmetry_nbd_other 0.194 r_nbd_refined 0.191 r_nbd_other 0.18 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.144 r_symmetry_xyhbond_nbd_refined 0.132 r_symmetry_nbd_refined 0.125 r_symmetry_nbtor_other 0.084 r_ncsr_local_group_1 0.066 r_chiral_restr 0.064 r_ext_dist_refined_b 0.056 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6692 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing Coot model building