3ODD

Comparison of the character and the speed of X-ray-induced structural changes of porcine pancreatic elastase at two temperatures, 100 and 15K. The data set was collected from region B of the crystal. Second step of radiation damage


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GVKPDB entry 1GVK

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291The initial concentration of the protein was 20 mg/ml in 10% glycerol solution. The reservoir contained a 250 mM Na2SO4, solution at pH 7.5 (adjusted with NaOH). For cryo-protection, the 250 mM Na2SO4 was supplemented with 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0840.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.987α = 90
b = 57.778β = 90
c = 74.585γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray15CCDADSC QUANTUM 3151.02-M FLAT MIRROR MADE OF ZERODUR PROVIDING VERTICAL FOCUSING AND REJECTION OF HARMONIC CONTAMINATION2008-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97895APS19-ID

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
11.15090.80.05619.648012626.72
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)
1.11.1492.10.197.63.68002

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB entry 1GVK1.19.8220.0579076396689.670.11980.11890.1377Random7.69
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]
-2.3239-5.3861-4.0219
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d18.7
f_angle_d1.206
f_chiral_restr0.111
f_bond_d0.011
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1822
Nucleic Acid Atoms
Solvent Atoms536
Heterogen Atoms11

Software

Software
Software NamePurpose
HKL-3000data collection
AMoREphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling