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Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other a structure obtained on MAD data
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 298 27.5% peg 3350, 100mM sodium acetate, pH 4.6, 250 mM ammonium acetate, 8% glycerol. Seeding., VAPOR DIFFUSION, HANGING DROP, temperature 298K 2 VAPOR DIFFUSION, HANGING DROP 4.6 298 peg 3350, ammonium acetate, sodium acetate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.978 α = 90 b = 43.266 β = 101.34 c = 55.553 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 4 mirrors 2000-05-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 ALS 5.0.2
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 1.65 20 97.3 0.036 37.8 3.11 18550 18049 16.4
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) 1.65 1.68 81.9 0.064 25.5 2.02 753
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MOLECULAR REPLACEMENT FREE R a structure obtained on MAD data 1.65 20 18533 17977 1775 97 0.1529 0.1529 0.1527 0.1518 0.2323 0.2226 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 1552
RMS Deviations Key Refinement Restraint Deviation s_non_zero_chiral_vol 0.05 s_similar_adp_cmpnt 0.05 s_zero_chiral_vol 0.03 s_from_restr_planes 0.025 s_angle_d 0.02 s_bond_d s_similar_dist s_anti_bump_dis_restr s_rigid_bond_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1437 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms 1
Software Software Software Name Purpose SHELXL-97 refinement CNS refinement SOLVE phasing DENZO data reduction SCALEPACK data scaling CNS phasing