☰ Navigation Tabs
Crystal structure of a putative peptidase (PARMER_02772) from Parabacteroides merdae ATCC 43184 at 2.26 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.2M ammonium dihydrogen phosphate, 50.0% 2-methyl-2,4-pentanediol, 4.0% Polypropylene Glycol P 400, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.42 49.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.333 α = 90 b = 131.213 β = 90.55 c = 129.056 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 KOHZU: Double Crystal Si(111) 2012-10-18 M SINGLE WAVELENGTH 0.918401, 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.918401 ALS 8.2.2
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 2.26 29.652 98.7 0.105 7.26 65894 -3 30.59
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 2.26 2.34 98.8 0.613 1.5
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 (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 2.26 29.652 65744 3335 99.88 0.1617 0.1593 0.1644 0.2061 0.2122 RANDOM 31.8058
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] -2.0065 -0.9017 -2.5007 4.5072
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.55 t_other_torsion 2.8 t_angle_deg 0.99 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_omega_torsion 3.55 t_other_torsion 2.8 t_angle_deg 0.99 t_bond_d 0.01 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9996 Nucleic Acid Atoms Solvent Atoms 619 Heterogen Atoms 122
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SOLVE phasing XSCALE data scaling BUSTER-TNT refinement XDS data reduction BUSTER refinement