1IM5

Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOthera structure obtained on MAD data

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.629827.5% peg 3350, 100mM sodium acetate, pH 4.6, 250 mM ammonium acetate, 8% glycerol. Seeding., VAPOR DIFFUSION, HANGING DROP, temperature 298K
2VAPOR DIFFUSION, HANGING DROP4.6298peg 3350, ammonium acetate, sodium acetate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.978α = 90
b = 43.266β = 101.34
c = 55.553γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2000-05-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.00ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.652097.30.03637.83.11185501804916.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.651.6881.90.06425.52.02753

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE Ra structure obtained on MAD data1.652018533179771775970.15290.15290.15270.2323RANDOM
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 MethodRefinement High ResolutionRefinement Low Resolution
1552
RMS Deviations
KeyRefinement Restraint Deviation
s_non_zero_chiral_vol0.05
s_similar_adp_cmpnt0.05
s_zero_chiral_vol0.03
s_from_restr_planes0.025
s_angle_d0.02
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 AtomsNumber
Protein Atoms1437
Nucleic Acid Atoms
Solvent Atoms128
Heterogen Atoms1

Software

Software
Software NamePurpose
SHELXL-97refinement
CNSrefinement
SOLVEphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing