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Crystal structure of an alpha-lytic protease prodomain-like protein (DESPIG_01740) from Desulfovibrio piger ATCC 29098 at 1.80 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.20M sodium acetate, 30.00% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.38 48.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.821 α = 90 b = 57.821 β = 90 c = 63.89 γ = 120
Symmetry Space Group P 32 2 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) 2012-09-19 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.979095,0.979338,0.953725 ALS 8.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 28.91 100 0.103 16.3 13.3 11856 11856 26.12
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 100 0.014 1.374 0.6 8 843
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 1.8 28.91 11834 562 99.97 0.1966 0.1953 0.2051 0.2228 0.2308 RANDOM 33.7023
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] 0.49 0.49 0.49 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.821 r_dihedral_angle_4_deg 18.443 r_dihedral_angle_3_deg 13.99 r_dihedral_angle_1_deg 5.462 r_angle_refined_deg 1.361 r_angle_other_deg 0.732 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.821 r_dihedral_angle_4_deg 18.443 r_dihedral_angle_3_deg 13.99 r_dihedral_angle_1_deg 5.462 r_angle_refined_deg 1.361 r_angle_other_deg 0.732 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 751 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 1
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SOLVE phasing SCALA data scaling REFMAC refinement MOSFLM data reduction