6QLA

CRYSTAL STRUCTURE OF THE PMGL2 ESTERASE (point mutant 1) FROM PERMAFROST METAGENOMIC LIBRARY


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6QIN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5288250mM Magnesium chloride, 12-18% PEG3350, 100mM HEPES pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.0740.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.14α = 90
b = 92.18β = 106.41
c = 74.46γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2017-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.00SPring-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
11.4356.46980.0750.0820.0330.99912.45.9110412
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)
11.431.4595.20.9591.060.4430.6265.5

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 REPLACEMENTTHROUGHOUT6QIN1.4356.46104774560697.760.15760.15620.184RANDOM18.001
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]
0.270.490.26-0.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.759
r_dihedral_angle_4_deg20.935
r_dihedral_angle_3_deg13.397
r_dihedral_angle_1_deg6.234
r_angle_refined_deg1.921
r_angle_other_deg1.691
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg24.759
r_dihedral_angle_4_deg20.935
r_dihedral_angle_3_deg13.397
r_dihedral_angle_1_deg6.234
r_angle_refined_deg1.921
r_angle_other_deg1.691
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4805
Nucleic Acid Atoms
Solvent Atoms577
Heterogen Atoms49

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction