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Crystal structure of co-catalytic metallopeptidase (YP_387682.1) from Desulfovibrio desulfuricans G20 at 1.60 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.1 277 NANODROP, 0.2M Sodium fluoride, 20.0% PEG 3350, No Buffer pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.44 49.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.85 α = 90 b = 82.19 β = 91.37 c = 89.34 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-06-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97901, 0.97926 SSRL BL11-1
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 27.995 98.7 0.045 9.92 3.28 101945 -3 18.5
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 1.66 94.5 0.314 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 1.6 27.995 101918 5090 99.4 0.155 0.154 0.1597 0.18 0.1886 RANDOM 14.803
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] 0.46 -0.75 0.17 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.953 r_dihedral_angle_4_deg 19.97 r_dihedral_angle_3_deg 12.784 r_scangle_it 6.736 r_dihedral_angle_1_deg 5.614 r_scbond_it 4.746 r_mcangle_it 2.642 r_mcbond_it 2.199 r_angle_refined_deg 1.624 r_angle_other_deg 1.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.953 r_dihedral_angle_4_deg 19.97 r_dihedral_angle_3_deg 12.784 r_scangle_it 6.736 r_dihedral_angle_1_deg 5.614 r_scbond_it 4.746 r_mcangle_it 2.642 r_mcbond_it 2.199 r_angle_refined_deg 1.624 r_angle_other_deg 1.007 r_mcbond_other 0.548 r_symmetry_vdw_other 0.256 r_nbd_refined 0.224 r_nbd_other 0.21 r_symmetry_hbond_refined 0.197 r_symmetry_vdw_refined 0.179 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.164 r_xyhbond_nbd_other 0.117 r_chiral_restr 0.103 r_nbtor_other 0.087 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5505 Nucleic Acid Atoms Solvent Atoms 916 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SOLVE phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction