6QIN

CRYSTAL STRUCTURE OF THE PMGL2 ESTERASE FROM PERMAFROST METAGENOMIC LIBRARY


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L1H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5288250mM Magnesium chloride, 12-18% PEG3350, 100mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.0740.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.01α = 90
b = 92.35β = 106.83
c = 74.23γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2016-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.656.3197.40.140.1530.0610.9857.86.177747
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6395.90.6530.7160.2880.8335.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3L1H1.656.3173837388397.250.15850.1570.1866RANDOM18.076
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]
0.420.82-0.13-0.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.749
r_dihedral_angle_4_deg21.213
r_dihedral_angle_3_deg13.626
r_dihedral_angle_1_deg6.436
r_angle_refined_deg2.299
r_angle_other_deg2.189
r_chiral_restr0.121
r_bond_refined_d0.018
r_gen_planes_refined0.014
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.749
r_dihedral_angle_4_deg21.213
r_dihedral_angle_3_deg13.626
r_dihedral_angle_1_deg6.436
r_angle_refined_deg2.299
r_angle_other_deg2.189
r_chiral_restr0.121
r_bond_refined_d0.018
r_gen_planes_refined0.014
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4731
Nucleic Acid Atoms
Solvent Atoms590
Heterogen Atoms3

Software

Software
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction