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Crystal structure of the sensor domain of BlaR1 from Staphylococcus aureus in its apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XA7 benzylpenicillin-acylated BlaR1 C-terminal domain, PDB entry 1XA7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.7 291 18-23% PEG 3350, 0.2M NaH2PO4, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.2 44.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.876 α = 90 b = 104.893 β = 107.79 c = 90.273 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 100 CCD ADSC QUANTUM 4 2003-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.10000 NSLS X8C
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 1.8 50 97.3 95274 95274
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.8 1.86 78
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 benzylpenicillin-acylated BlaR1 C-terminal domain, PDB entry 1XA7 1.8 50 95247 90477 4770 97.09 0.18824 0.18824 0.18618 0.1938 0.2271 0.2335 RANDOM 18.616
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] 0.11 0.1 -0.3 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.9 r_scangle_it 3.335 r_scbond_it 2.044 r_mcangle_it 1.393 r_angle_refined_deg 1.296 r_angle_other_deg 0.767 r_mcbond_it 0.753 r_symmetry_vdw_other 0.28 r_symmetry_vdw_refined 0.258 r_nbd_other 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.9 r_scangle_it 3.335 r_scbond_it 2.044 r_mcangle_it 1.393 r_angle_refined_deg 1.296 r_angle_other_deg 0.767 r_mcbond_it 0.753 r_symmetry_vdw_other 0.28 r_symmetry_vdw_refined 0.258 r_nbd_other 0.24 r_nbd_refined 0.212 r_symmetry_hbond_refined 0.206 r_xyhbond_nbd_refined 0.18 r_nbtor_other 0.083 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.006 r_bond_other_d 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 8135 Nucleic Acid Atoms Solvent Atoms 1031 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing