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Mutant (S106A) Escherichia coli L,D-carboxypeptidase A (LdcA)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.02M Tris Cl pH 8.5, 0.2M sodium thiocyanate, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.02 38.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.823 α = 90 b = 93.379 β = 90 c = 86.793 γ = 90
Symmetry Space Group P 21 21 2
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 300K 2016-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 46.7 99.1 0.097 0.057 0.999 11.2 6.5 56189
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.77 85 0.832 0.368 0.491 2 5.5
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 (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 1.755 46.689 56144 2765 99.105 0.229 0.2274 0.2351 0.2691 0.2715 RANDOM 32.487
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] 3.709 -2.707 -1.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.909 r_dihedral_angle_4_deg 21.093 r_dihedral_angle_3_deg 14.405 r_lrange_it 7.406 r_lrange_other 7.405 r_dihedral_angle_1_deg 6.956 r_scangle_it 5.616 r_scangle_other 5.615 r_mcangle_it 4.185 r_mcangle_other 4.184
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.909 r_dihedral_angle_4_deg 21.093 r_dihedral_angle_3_deg 14.405 r_lrange_it 7.406 r_lrange_other 7.405 r_dihedral_angle_1_deg 6.956 r_scangle_it 5.616 r_scangle_other 5.615 r_mcangle_it 4.185 r_mcangle_other 4.184 r_scbond_it 3.662 r_scbond_other 3.662 r_mcbond_it 2.89 r_mcbond_other 2.89 r_angle_refined_deg 1.902 r_angle_other_deg 1.081 r_symmetry_xyhbond_nbd_refined 0.304 r_nbd_other 0.268 r_xyhbond_nbd_other 0.251 r_symmetry_nbd_refined 0.248 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.182 r_nbtor_refined 0.176 r_symmetry_nbd_other 0.167 r_chiral_restr 0.116 r_symmetry_nbtor_other 0.082 r_symmetry_xyhbond_nbd_other 0.047 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4429 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHENIX phasing