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Crystal structure of a putative gamma-d-glutamyl-l-diamino acid endopeptidase (npun_r0659) from nostoc punctiforme pcc 73102 at 1.79 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 1.4M Na3Citrate, 0.1M HEPES, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.43 63.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.08 α = 90 b = 125.08 β = 90 c = 97.67 γ = 90
Symmetry Space Group P 41 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 CCD ADSC QUANTUM 210 2005-09-28 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0163, 0.9798 ALS 8.2.1
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 1.79 29.48 97.5 0.147 12.56 7.4 72488
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 1.79 1.86 89.4 89.4 0.01146 2.13 6.5
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 MAD THROUGHOUT 1.79 29.48 68770 3659 99.55 0.155 0.154 0.1644 0.172 0.1867 RANDOM 22.209
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] 0.37 0.37 -0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.222 r_dihedral_angle_4_deg 14.612 r_dihedral_angle_3_deg 12.46 r_scangle_it 6.639 r_dihedral_angle_1_deg 5.661 r_scbond_it 5.072 r_mcangle_it 2.896 r_mcbond_it 2.06 r_angle_refined_deg 1.513 r_angle_other_deg 0.891
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.222 r_dihedral_angle_4_deg 14.612 r_dihedral_angle_3_deg 12.46 r_scangle_it 6.639 r_dihedral_angle_1_deg 5.661 r_scbond_it 5.072 r_mcangle_it 2.896 r_mcbond_it 2.06 r_angle_refined_deg 1.513 r_angle_other_deg 0.891 r_mcbond_other 0.495 r_symmetry_vdw_other 0.267 r_symmetry_vdw_refined 0.224 r_nbd_refined 0.214 r_nbtor_refined 0.192 r_nbd_other 0.185 r_symmetry_hbond_refined 0.161 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.094 r_nbtor_other 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3426 Nucleic Acid Atoms Solvent Atoms 428 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction SOLVE phasing