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Structure of the BIG_1156.2 domain of putative penicillin-binding protein MrcA from Nitrosomonas europaea ATCC 19718
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 0.1M MES pH 6.5, 30% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.31 46.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.206 α = 90 b = 52.219 β = 107.87 c = 56.86 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 315 2007-07-15 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97959, 0.97970 APS 19-ID
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 1.6 50 98.8 0.069 9.8 6.9 27910 27910 -3 18.9
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 1.6 1.68 97.2 0.347 3.3 4.6 1823
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.64 35.67 26155 26155 1316 99.71 0.173 0.173 0.17 0.217 0.2565 RANDOM 17.161
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] 0.25 0.66 0.68 -0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.216 r_dihedral_angle_3_deg 14.352 r_dihedral_angle_4_deg 9.716 r_dihedral_angle_1_deg 5.798 r_scangle_it 4.068 r_scbond_it 2.799 r_mcangle_it 1.781 r_angle_refined_deg 1.641 r_mcbond_it 1.512 r_angle_other_deg 0.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.216 r_dihedral_angle_3_deg 14.352 r_dihedral_angle_4_deg 9.716 r_dihedral_angle_1_deg 5.798 r_scangle_it 4.068 r_scbond_it 2.799 r_mcangle_it 1.781 r_angle_refined_deg 1.641 r_mcbond_it 1.512 r_angle_other_deg 0.952 r_mcbond_other 0.32 r_symmetry_vdw_other 0.266 r_nbd_refined 0.221 r_nbd_other 0.202 r_symmetry_vdw_refined 0.171 r_nbtor_refined 0.17 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.101 r_nbtor_other 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1628 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 11
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building